From 70e9102cc0f6f7fae7f5f81daf2e02a5e118ebbe Mon Sep 17 00:00:00 2001 From: TeresasaZ Date: Sun, 2 Mar 2025 21:49:07 -0500 Subject: [PATCH 01/14] mfinder second commit, most functions moved to util file. Modified interactions file, added mfinder utils file, modified test interactions file. --- api/resources/interactions.py | 26 +++- api/utils/mfinder_utils.py | 200 +++++++++++++++++++++++++++ tests/resources/test_interactions.py | 55 ++++++++ 3 files changed, 280 insertions(+), 1 deletion(-) create mode 100644 api/utils/mfinder_utils.py diff --git a/api/resources/interactions.py b/api/resources/interactions.py index 81688760..7fa2c9e9 100644 --- a/api/resources/interactions.py +++ b/api/resources/interactions.py @@ -5,9 +5,10 @@ """ from flask_restx import Namespace, Resource, fields -from flask import request +from flask import request, jsonify from markupsafe import escape from api.utils.bar_utils import BARUtils +from api.utils.mfinder_utils import MfinderUtils from marshmallow import Schema, ValidationError, fields as marshmallow_fields from api import db from api.models.rice_interactions import Interactions as RiceInteractions @@ -156,3 +157,26 @@ def post(self): return BARUtils.success_exit(res) else: return BARUtils.error_exit("No data for the given species/genes"), 400 + + +@itrns.route("/mfinder") +class MFinder(Resource): + @itrns.expect(post_int_data) + def post(self): + """This endpoint was originally written by Vincent Lau to return mFinder + results to AGENT in his express node.JS app. However Tianhui Zhao refactored + to the BAR_API + """ + data = request.get_json() + # Validate json + try: + data = MFinderDataSchema().load(data) + except ValidationError as err: + return BARUtils.error_exit(err.messages), 400 + + filtered_valid_arr = MfinderUtils.input_validation(data["data"]) + if isinstance(filtered_valid_arr, str): + return BARUtils.error_exit(filtered_valid_arr), 400 + settings = MfinderUtils.settings_validation(data.get("options", {})) + ret_json = MfinderUtils.create_files_and_mfinder(filtered_valid_arr, settings) + return jsonify(MfinderUtils.beautify_results(ret_json)) diff --git a/api/utils/mfinder_utils.py b/api/utils/mfinder_utils.py new file mode 100644 index 00000000..46d517d7 --- /dev/null +++ b/api/utils/mfinder_utils.py @@ -0,0 +1,200 @@ +from api.utils.bar_utils import BARUtils + +import tempfile +import os +import subprocess +from collections import defaultdict + + +class MfinderUtils: + + @staticmethod + # Eliminates same pairs + def uniq_with(arr, comp_func): + unique_arr = [] + for item in arr: + if not any(comp_func(item, unique_item) for unique_item in unique_arr): + unique_arr.append(item) + return unique_arr + + @staticmethod + def is_equal(a, b): + return a == b + + @staticmethod + def find_key(d, value): + return next(key for key, val in d.items() if val == value) + + # Check if JSON body data obj is an array of arrays (2d arr) + # ex [ [ "AT1G010100", "AT5G01010" ], ["AT3G10000", "AT2G03240"]] + # {Array>} input: the above arr + @staticmethod + def input_validation(input): + if not isinstance(input, list): + return "invalid JSON, not an arr" + + if len(input) == 0: + return "arr length 0!" + + if any(len(i) != 2 for i in input): + return "inner arr length is not of length 2!" + + if not all(isinstance(i, list) for i in input): + return "invalid JSON, check arr members are arrs!" + + if not all(isinstance(j, str) for i in input for j in i): + return "invalid JSON, check if inside arr members are strings!" + + if not all(BARUtils.is_arabidopsis_gene_valid(j) for i in input for j in i): + return "Invalid gene ID contained!" + + # filter self-edges and duplicate edges (mFinder does not accept) + return MfinderUtils.uniq_with([i for i in input if i[0] != i[1]], MfinderUtils.is_equal) + + # Some mFinders params allowed within reasonable server load. Namely mFinder takes 3 basic params: nd (non-directed network), + # r (# of rand networks to gen), s (motif size), u (unique min), z (z-score min). The defaults are directed, 100, 3, 4, & 2 + # respectively. HOWEVER choose r of 30 for speed + # Do a validation check on each value too! + # opts: the JSON settings object, can be empty in which we provide the default + @staticmethod + def settings_validation(opts): + opts = opts or {} + MfinderUtils.injection_check(opts) + settings_obj = opts.copy() + if "nd" not in opts: + settings_obj["nd"] = False + elif not isinstance(opts["nd"], bool): + return "incorrect nd setting - is it boolean?", 400 + + if "r" not in opts: + settings_obj["r"] = 50 + elif not isinstance(opts["r"], int) or opts["r"] > 150: + return "incorrect r setting - is it a number under 151?", 400 + + if "s" not in opts: + settings_obj["s"] = 3 + elif not isinstance(opts["s"], int) or opts["s"] < 2 or opts["s"] > 4: + return "incorrect s setting - is it a number between 2 and 4?", 400 + + if "u" not in opts: + settings_obj["u"] = 4 + elif not isinstance(opts["u"], int) or opts["u"] > 999: + return "incorrect u setting - is it a number or below 1000?", 400 + + if "z" not in opts: + settings_obj["z"] = 2 + elif not isinstance(opts["z"], int) or opts["z"] > 99: + return "incorrect z setting - is it a number or below 100?", 400 + + return settings_obj + + # Check for injection, throw if suspiciously long command is found. + # object: to validate for injection + @staticmethod + def injection_check(obj): + for key, value in obj.items(): + if len(str(value)) > 10: + return f"{key} settings param is too long", 400 + + # Take in the filtered array of gene-id pairs (edges) and perform + # mFinder analysis on them (create temp text files to do so) + # Performed SYNCHRONOUSLY !!! + @staticmethod + def create_files_and_mfinder(input, opts_obj): + + # give read/write permissions to user but nada to anybody else + tmpfile = tempfile.NamedTemporaryFile(mode="w+", suffix=".txt", delete=False) + os.chmod(tmpfile.name, 0o600) + + # get a hash of IDs -> numbers for later lookup and writable string + hash_of_ids, return_str = MfinderUtils.get_gene_id_hash_map(input) + + # write to temp file which mFinder will run/read on + tmpfile.write(return_str) + tmpfile.flush() + + # file_path = "/usr/src/app/mfinder/mfinder1.21_1/mfinder" + + # if os.access(file_path, os.X_OK): + # return (f"The file exists {tmpfile.name}") + # else: + # return "The file does not exist" + + command = ( + f"/bartmp/mfinder {tmpfile.name} " + f"-s {opts_obj['s']} " + f"-r {opts_obj['r']} " + f"-u {opts_obj['u']} " + f"-z {opts_obj['z']} " + f"{'-nd ' if opts_obj.get('nd') else ''}" + "-omem" + ) + subprocess.run(command, shell=True, check=True) + + with open(tmpfile.name[:-4] + "_OUT.txt", "r") as stats_file: + mfinder_stats = stats_file.read() + + with open(tmpfile.name[:-4] + "_MEMBERS.txt", "r") as members_file: + mfinder_members = members_file.read() + + tmpfile.close() + print(f"Temporary file: {tmpfile.name}") + os.remove(tmpfile.name) + + return {"hashOfIds": hash_of_ids, "mFinderStats": mfinder_stats, "mFinderMembers": mfinder_members} + + # Take an input of array of array of strings which represent edges and transform those gene IDs (unique!) to a hash table and + # coinciding edges i.e. [["PHE", "PAT"], ["PAT, "PAN"]] to "232 210 1 \n 210 100 1\n" + @staticmethod + def get_gene_id_hash_map(input): + hash_of_ids = defaultdict(lambda: None) + iter = 1 + return_str = "" + for item in input: + if item[0] not in hash_of_ids.values(): + hash_of_ids[iter] = item[0] + iter += 1 + if item[1] not in hash_of_ids.values(): + hash_of_ids[iter] = item[1] + iter += 1 + return_str += f"{MfinderUtils.find_key(hash_of_ids, item[0])} {MfinderUtils.find_key(hash_of_ids, item[1])} 1\n" + + return hash_of_ids, return_str + + # Beautify the output file string and members file string + @staticmethod + def beautify_results(mfinder_res_obj): + stats = mfinder_res_obj["mFinderStats"] + mems = mfinder_res_obj["mFinderMembers"] + id_map = mfinder_res_obj["hashOfIds"] + ret_obj = {"sigMotifs": {}, "motifList": {}} + + try: + sig_motifs_str = stats.split("[MILI]\t\n\n")[1].split("Full")[0].split("\n\n") + # In case stats has less than 2 parts after split('[MILI]\t\n\n')[1] + except IndexError: + raise ValueError("Expected delimiter '[MILI]\t\n\n' or 'Full' not found in the stats string.") + sig_motifs_str = sig_motifs_str[: len(sig_motifs_str) - 2 : 2] + for item in sig_motifs_str: + split_stats_for_motif_id = item.split("\t") + ret_obj["sigMotifs"][split_stats_for_motif_id[0]] = { + "numAppearances": split_stats_for_motif_id[1], + "numAppearancesRand": split_stats_for_motif_id[2], + "appearancesZScore": split_stats_for_motif_id[3], + "pValue": split_stats_for_motif_id[4], + "uniq": split_stats_for_motif_id[5], + "conc": split_stats_for_motif_id[6], + } + + subgraphs_list_str = mems.split("subgraph id = ")[1:] + for subgraph_str in subgraphs_list_str: + member_list_split = subgraph_str.split("\n") + motif_mem_list = [i.rstrip("\t") for i in member_list_split[5:-2]] + motif_mem_results = [] + for i in motif_mem_list: + three_genes = i.split("\t") + formatted_str = f"{id_map[int(three_genes[0])]}\t{id_map[int(three_genes[1])]}\t{id_map[int(three_genes[2])]}" # i.e. PAT\tPAN\tEGFR + motif_mem_results.append(formatted_str) + ret_obj["motifList"][member_list_split[0]] = motif_mem_results + + return BARUtils.success_exit(ret_obj) diff --git a/tests/resources/test_interactions.py b/tests/resources/test_interactions.py index 3f089b41..fdb3a2b8 100644 --- a/tests/resources/test_interactions.py +++ b/tests/resources/test_interactions.py @@ -1,6 +1,7 @@ from api import app from unittest import TestCase import json +from json import load class TestIntegrations(TestCase): @@ -131,3 +132,57 @@ def test_post_itrns(self): "error": "No data for the given species/genes", } self.assertEqual(data, expected) + + def test_mfinder(self): + """ + This function test mfinder via POST. + """ + # Valid request + with open("tests/data/mfinder_input.json") as json_file_1: + input_data = load(json_file_1) + response = self.app_client.post( + "/interactions/mfinder", + json=input_data, + ) + data = json.loads(response.get_data(as_text=True)) + with open("tests/data/mfinder_output.json") as json_file_2: + expected = load(json_file_2) + self.assertEqual(data, expected) + + # Invalid data structure + response = self.app_client.post("/interactions/mfinder", json={"data": {}}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": ["Not a valid list."]}} + self.assertEqual(data, expected) + + response = self.app_client.post("/interactions/mfinder", json={"data": []}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "arr length 0!"} + self.assertEqual(data, expected) + + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420"]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "inner arr length is not of length 2!"} + self.assertEqual(data, expected) + + response = self.app_client.post("/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], 1]}) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": {"1": ["Not a valid list."]}}} + self.assertEqual(data, expected) + + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420", 1]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": {"data": {"1": {"1": ["Not a valid string."]}}}} + self.assertEqual(data, expected) + + # Invalid gene ID + response = self.app_client.post( + "/interactions/mfinder", json={"data": [["AT1G01010", "AT5G01010"], ["001G01030", "AT2G03240"]]} + ) + data = json.loads(response.get_data(as_text=True)) + expected = {"wasSuccessful": False, "error": "Invalid gene ID contained!"} + self.assertEqual(data, expected) From 5fe69dd8a30d005992eed4c1ffdb51eb07ecf081 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 22 Mar 2025 16:12:04 -0400 Subject: [PATCH 02/14] Add Support of SNP query of Canola and add new endpoint for Homolog query (only support Arabidopsis and Brassica napus now) --- api/models/canola_nssnp.py | 36 ++++ api/models/homologs_db.py | 14 ++ api/resources/snps.py | 155 +++++++++++---- config/BAR_API.cfg | 4 +- config/databases/canola_nssnp.sql | 183 ++++++++++++++++++ config/databases/homologs_db.sql | 120 ++++++++++++ config/init.sh | 2 + .../data/get_canola_homolog_information.json | 47 +++++ tests/resources/test_snps.py | 77 ++++++++ 9 files changed, 604 insertions(+), 34 deletions(-) create mode 100755 api/models/canola_nssnp.py create mode 100644 api/models/homologs_db.py mode change 100644 => 100755 config/BAR_API.cfg create mode 100755 config/databases/canola_nssnp.sql create mode 100755 config/databases/homologs_db.sql create mode 100644 tests/data/get_canola_homolog_information.json diff --git a/api/models/canola_nssnp.py b/api/models/canola_nssnp.py new file mode 100755 index 00000000..ac63582e --- /dev/null +++ b/api/models/canola_nssnp.py @@ -0,0 +1,36 @@ +from typing import Optional +from api import db +#from sqlalchemy.ext.declarative import declarative_base + +#CanolaBase = declarative_base() +class CanolaProteinReference(db.Model): + __bind_key__ = "canola_nssnp" + __tablename__ = "protein_reference" + + protein_reference_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + gene_identifier: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + gene_name: db.Mapped[Optional[str]] = db.mapped_column(db.String(45), nullable=True) + + proteinsJoin = db.relationship("CanolaSnpsToProtein", backref="protein", cascade="all, delete-orphan") + + +class CanolaSnpsToProtein(db.Model): + __bind_key__ = "canola_nssnp" + __tablename__ = "snps_to_protein" + + snps_reference_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + protein_reference_id: db.Mapped[int] = db.mapped_column( + db.Integer(), db.ForeignKey("protein_reference.protein_reference_id", ondelete="CASCADE"), primary_key=True + ) + transcript_pos: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + chromosome: db.Mapped[str] = db.mapped_column(db.String(25), nullable=False) + chromosomal_loci: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + ref_DNA: db.Mapped[str] = db.mapped_column(db.String(1), nullable=False) + alt_DNA: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + aa_pos: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + ref_aa: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) + alt_aa: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) + type: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False) + effect_impact: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False) + transcript_biotype: db.Mapped[Optional[str]] = db.mapped_column(db.String(45), nullable=True) + alt_freq: db.Mapped[float] = db.mapped_column(db.Numeric(10, 5), nullable=False) diff --git a/api/models/homologs_db.py b/api/models/homologs_db.py new file mode 100644 index 00000000..7b0d985d --- /dev/null +++ b/api/models/homologs_db.py @@ -0,0 +1,14 @@ +from api import db + + +class homologs(db.Model): + __bind_key__ = "homologs_db" + __tablename__ = 'homologs' + + homologs_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + search_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + result_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + search_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + result_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + Percent_id: db.Mapped[float] = db.mapped_column(db.Numeric(10,5), nullable=False) + e_score: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False) diff --git a/api/resources/snps.py b/api/resources/snps.py index 112c11de..721943bd 100755 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -17,6 +17,11 @@ SnpsReference as SoybeanSnpsReference, SamplesLookup as SoybeanSampleNames, ) +from api.models.canola_nssnp import ( + CanolaProteinReference as CanolaProteinReference, + CanolaSnpsToProtein as CanolaSnpsToProtein +) +from api.models.homologs_db import homologs as HomologsDB from api.utils.bar_utils import BARUtils from flask import request import re @@ -141,7 +146,7 @@ class GeneNameAlias(Resource): def get(self, species="", gene_id=""): """Endpoint returns annotated SNP poplar data in order of (to match A th API format): AA pos (zero-indexed), sample id, 'missense_variant','MODERATE', 'MISSENSE', codon/DNA base change, - AA change (DH), pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype + AA change (DH), pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype (allele frequency for canola) values with single quotes are fixed""" results_json = [] @@ -160,43 +165,76 @@ def get(self, species="", gene_id=""): protein_reference = SoybeanProteinReference snps_to_protein = SoybeanSnpsToProtein snps_reference = SoybeanSnpsReference + elif species == "canola" and BARUtils.is_canola_gene_valid(gene_id): + protein_reference = CanolaProteinReference + snps_to_protein = CanolaSnpsToProtein else: return BARUtils.error_exit("Invalid gene id"), 400 - rows = ( - db.session.execute( - db.select(protein_reference, snps_to_protein, snps_reference) - .select_from(protein_reference) - .join(snps_to_protein) - .join(snps_reference) - .where(protein_reference.gene_identifier == gene_id) + if species == "canola" and BARUtils.is_canola_gene_valid(gene_id): + rows = ( + db.session.execute( + db.select(protein_reference, snps_to_protein) + .select_from(protein_reference) + .join(snps_to_protein) + .where(protein_reference.gene_identifier == gene_id) + ) + .tuples() + .all() + ) + for protein, snptoprotein in rows: + itm_lst = [ + snptoprotein.chromosome, + snptoprotein.aa_pos - 1, # zero index-ed + None, + "missense_variant", + "MODERATE", + "MISSENSE", + str(snptoprotein.transcript_pos) + snptoprotein.ref_DNA + ">" + snptoprotein.alt_DNA, + snptoprotein.ref_aa + snptoprotein.alt_aa, + None, + gene_id, + "protein_coding", + "CODING", + protein.gene_name, + float(snptoprotein.alt_freq), + ] + results_json.append(itm_lst) + else: + rows = ( + db.session.execute( + db.select(protein_reference, snps_to_protein, snps_reference) + .select_from(protein_reference) + .join(snps_to_protein) + .join(snps_reference) + .where(protein_reference.gene_identifier == gene_id) + ) + .tuples() + .all() ) - .tuples() - .all() - ) - # BAR A Th API format is chr, AA pos (zero-indexed), sample id, 'missense_variant', - # 'MODERATE', 'MISSENSE', codon/DNA base change, AA change (DH), - # pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype - for protein, snpsjoin, snpstbl in rows: - itm_lst = [ - snpstbl.chromosome, - # snpstbl.chromosomal_loci, - snpsjoin.aa_pos - 1, # zero index-ed - snpstbl.sample_id, - "missense_variant", - "MODERATE", - "MISSENSE", - str(snpsjoin.transcript_pos) + snpsjoin.ref_DNA + ">" + snpsjoin.alt_DNA, - snpsjoin.ref_aa + snpsjoin.alt_aa, - None, - re.sub(r".\d$", "", protein.gene_identifier), - "protein_coding", - "CODING", - protein.gene_identifier, - None, - ] - results_json.append(itm_lst) + # BAR A Th API format is chr, AA pos (zero-indexed), sample id, 'missense_variant', + # 'MODERATE', 'MISSENSE', codon/DNA base change, AA change (DH), + # pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype + for protein, snpsjoin, snpstbl in rows: + itm_lst = [ + snpstbl.chromosome, + # snpstbl.chromosomal_loci, + snpsjoin.aa_pos - 1, # zero index-ed + snpstbl.sample_id, + "missense_variant", + "MODERATE", + "MISSENSE", + str(snpsjoin.transcript_pos) + snpsjoin.ref_DNA + ">" + snpsjoin.alt_DNA, + snpsjoin.ref_aa + snpsjoin.alt_aa, + None, + re.sub(r".\d$", "", protein.gene_identifier), + "protein_coding", + "CODING", + protein.gene_identifier, + None, + ] + results_json.append(itm_lst) # Return results if there are data if len(results_json) > 0: @@ -502,3 +540,54 @@ def get(self, pval="", araid="", popid=""): pop_both_sig_idx = HotspotUtils.get_sig_index(pop_both_sig) output = {"ara_id": araid, "pop_id": popid, "ara_hotspots": ara_both_sig_idx, "pop_hotspots": pop_both_sig_idx} return BARUtils.success_exit(output) + + +@snps.route("/homologs///") +class SeqHotspots(Resource): + @snps.param("search_species", _in="path", default="canola") + @snps.param("search_gene", _in="path", default="BnaA07g31480D") + @snps.param("target_species", _in="path", default="arabidopsis") + def get(self, search_species="", search_gene="", target_species=""): + """This endpoint shows the homologs proteins of search_gene in target_species. + The endpoint returns a list of homologous pairs of proteins in following format: + Percent_id(percent identity get by blast); e score + """ + # Escape input + search_species = escape(search_species) + gene_id = escape(search_gene) + target_species = escape(target_species) + supported = ["arabidopsis", "canola"] + if (search_species not in supported) or (target_species not in supported): + return BARUtils.error_exit("Species not supported"), 400 + elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or \ + (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)): + results = HomologsDB.query.filter_by( + search_protein_name=gene_id, + search_species_name=search_species, + result_species_name=target_species + ).all() + if not results: + return BARUtils.error_exit("No homologs found for the given query"), 400 + + homologs_list = [ + { + "search_species_name": search_species, + "search_protein_name": gene_id, + "result_species_name": target_species, + "result_protein_name": homolog.result_protein_name, + "Percent_id": float(homolog.Percent_id), + "e_score": float(homolog.e_score) + } + for homolog in results + ] + homologs_list.sort(key=lambda x: x["e_score"]) + if len(homologs_list) >= 5: homologs_list = homologs_list[:5] + response = { + "homologs": homologs_list + } + + return BARUtils.success_exit(response), 200 + else: + return BARUtils.error_exit("Invalid gene id"), 400 + + diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg old mode 100644 new mode 100755 index f6e0ab22..5210e706 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -40,5 +40,7 @@ SQLALCHEMY_BINDS = { 'striga' : 'mysql://root:root@localhost/striga', 'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp', 'tomato_sequence' : 'mysql://root:root@localhost/tomato_sequence', - 'triphysaria' : 'mysql://root:root@localhost/triphysaria' + 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', + 'homologs_db' : 'mysql://root:root@localhost/homologs_db' + } diff --git a/config/databases/canola_nssnp.sql b/config/databases/canola_nssnp.sql new file mode 100755 index 00000000..a89d10dd --- /dev/null +++ b/config/databases/canola_nssnp.sql @@ -0,0 +1,183 @@ +SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0; +SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0; +SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION'; + +-- ----------------------------------------------------- +-- Schema nov24_canola_snps +-- ----------------------------------------------------- +DROP SCHEMA IF EXISTS `canola_nssnp` ; + +-- ----------------------------------------------------- +-- Schema nov24_canola_snps +-- ----------------------------------------------------- +CREATE SCHEMA IF NOT EXISTS `canola_nssnp` DEFAULT CHARACTER SET utf8 ; +USE `canola_nssnp` ; + +-- ----------------------------------------------------- +-- Table `canola_nssnp`.`protein_reference` +-- ----------------------------------------------------- +DROP TABLE IF EXISTS `canola_nssnp`.`protein_reference` ; + +create table protein_reference +( + protein_reference_id int auto_increment + primary key, + gene_identifier varchar(45) not null, + gene_name varchar(45) null +); + +-- ----------------------------------------------------- +-- Table `canola_nssnp`.`snps_to_protein` +-- ----------------------------------------------------- +DROP TABLE IF EXISTS `canola_nssnp`.`snps_to_protein` ; + +create table snps_to_protein +( + snps_reference_id int auto_increment, + protein_reference_id int not null, + transcript_pos int not null, + chromosome varchar(25) not null, + chromosomal_loci int not null, + ref_DNA varchar(1) not null, + alt_DNA varchar(45) not null, + aa_pos int not null, + ref_aa varchar(3) not null, + alt_aa varchar(3) not null, + type varchar(50) not null, + effect_impact varchar(50) not null, + transcript_biotype varchar(45) null, + alt_freq decimal(10, 5) not null, + primary key (snps_reference_id, protein_reference_id), + constraint protein_fk + foreign key (protein_reference_id) references protein_reference (protein_reference_id) +); + +create index protein_fk_idx + on snps_to_protein (protein_reference_id); + + +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (1, 'GSBRNA2T00000001001', 'BnaC09g12820D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (2, 'GSBRNA2T00000003001', 'BnaC09g12810D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (3, 'GSBRNA2T00000005001', 'BnaC09g12800D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (4, 'GSBRNA2T00000007001', 'BnaC09g12790D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (5, 'GSBRNA2T00000008001', 'BnaC09g12780D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (6, 'GSBRNA2T00000009001', 'BnaC09g12770D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (7, 'GSBRNA2T00000011001', 'BnaC09g12760D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (8, 'GSBRNA2T00000012001', 'BnaC09g12750D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (9, 'GSBRNA2T00000015001', 'BnaC09g12740D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (10, 'GSBRNA2T00000016001', 'BnaC09g12730D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (63265, 'GSBRNA2T00102721001', 'BnaA07g31480D'); + +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142004, 63265, 52, 'chrA07', 21985117, 'A', 'C', 18, 'Met', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142005, 63265, 130, 'chrA07', 21985679, 'G', 'T', 44, 'Gly', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.04930); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142006, 63265, 163, 'chrA07', 21985712, 'C', 'G', 55, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.09210); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142007, 63265, 268, 'chrA07', 21985817, 'G', 'A', 90, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142008, 63265, 284, 'chrA07', 21985833, 'G', 'C', 95, 'Arg', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142009, 63265, 433, 'chrA07', 21985982, 'C', 'T', 145, 'Pro', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142010, 63265, 442, 'chrA07', 21985991, 'G', 'A', 148, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142011, 63265, 445, 'chrA07', 21985994, 'A', 'G', 149, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142012, 63265, 486, 'chrA07', 21986035, 'C', 'G', 162, 'His', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.08310); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142013, 63265, 500, 'chrA07', 21986049, 'T', 'G', 167, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08140); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142014, 63265, 526, 'chrA07', 21986075, 'G', 'A', 176, 'Gly', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08390); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142015, 63265, 541, 'chrA07', 21986090, 'T', 'C', 181, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142016, 63265, 634, 'chrA07', 21986183, 'C', 'A', 212, 'Leu', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142017, 63265, 640, 'chrA07', 21986189, 'C', 'T', 214, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142018, 63265, 694, 'chrA07', 21986243, 'G', 'T', 232, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142019, 63265, 769, 'chrA07', 21986318, 'T', 'C', 257, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.05180); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142020, 63265, 848, 'chrA07', 21986397, 'G', 'A', 283, 'Ser', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.05100); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142021, 63265, 859, 'chrA07', 21986408, 'T', 'C', 287, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.05920); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142022, 63265, 889, 'chrA07', 21986438, 'A', 'G', 297, 'Lys', 'Glu', 'missense_variant', 'MODERATE', 'protein_coding', 0.06330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142023, 63265, 979, 'chrA07', 21986528, 'C', 'G', 327, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142024, 63265, 995, 'chrA07', 21986544, 'C', 'T', 332, 'Thr', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142025, 63265, 1039, 'chrA07', 21986588, 'C', 'T', 347, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.07070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142026, 63265, 1042, 'chrA07', 21986591, 'T', 'C', 348, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142027, 63265, 1060, 'chrA07', 21986609, 'A', 'G', 354, 'Asn', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142028, 63265, 1075, 'chrA07', 21986624, 'T', 'C', 359, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142029, 63265, 1267, 'chrA07', 21986816, 'C', 'G', 423, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.07240); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142030, 63265, 1336, 'chrA07', 21986885, 'C', 'G', 446, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142031, 63265, 1363, 'chrA07', 21986912, 'G', 'A', 455, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.32150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142032, 63265, 1420, 'chrA07', 21986969, 'T', 'A', 474, 'Ser', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01810); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142033, 63265, 1462, 'chrA07', 21987011, 'C', 'G', 488, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.04610); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142034, 63265, 1595, 'chrA07', 21987144, 'A', 'C', 532, 'Glu', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.04440); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142035, 63265, 1735, 'chrA07', 21987284, 'C', 'G', 579, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.29930); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142036, 63265, 1744, 'chrA07', 21987293, 'T', 'C', 582, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.02380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142037, 63265, 1865, 'chrA07', 21987414, 'C', 'T', 622, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142038, 63265, 2077, 'chrA07', 21987626, 'C', 'G', 693, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142039, 63265, 2086, 'chrA07', 21987635, 'C', 'A', 696, 'His', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142040, 63265, 2089, 'chrA07', 21987638, 'A', 'G', 697, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142041, 63265, 2215, 'chrA07', 21987764, 'A', 'T', 739, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142042, 63265, 2227, 'chrA07', 21987776, 'G', 'C', 743, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142043, 63265, 2233, 'chrA07', 21987782, 'T', 'C', 745, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142044, 63265, 2254, 'chrA07', 21987803, 'C', 'T', 752, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142045, 63265, 2323, 'chrA07', 21987872, 'T', 'C', 775, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.28040); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142046, 63265, 2350, 'chrA07', 21987899, 'G', 'A', 784, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142047, 63265, 2395, 'chrA07', 21987944, 'C', 'G', 799, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142048, 63265, 2425, 'chrA07', 21987974, 'G', 'C', 809, 'Val', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142049, 63265, 2434, 'chrA07', 21987983, 'A', 'G', 812, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142050, 63265, 2446, 'chrA07', 21987995, 'A', 'G', 816, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142051, 63265, 2464, 'chrA07', 21988013, 'A', 'C', 822, 'Ser', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27140); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142052, 63265, 2518, 'chrA07', 21988067, 'C', 'G', 840, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142053, 63265, 2521, 'chrA07', 21988070, 'T', 'G', 841, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.24180); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142054, 63265, 2545, 'chrA07', 21988094, 'G', 'A', 849, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.31830); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142055, 63265, 2596, 'chrA07', 21988145, 'A', 'G', 866, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.26320); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142056, 63265, 2632, 'chrA07', 21988181, 'T', 'C', 878, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26730); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142057, 63265, 2737, 'chrA07', 21988286, 'G', 'A', 913, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26640); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142058, 63265, 2770, 'chrA07', 21988319, 'G', 'A', 924, 'Val', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.27220); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142059, 63265, 2800, 'chrA07', 21988349, 'C', 'T', 934, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142060, 63265, 2848, 'chrA07', 21988397, 'T', 'C', 950, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142061, 63265, 2878, 'chrA07', 21988427, 'T', 'C', 960, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142062, 63265, 2881, 'chrA07', 21988430, 'C', 'T', 961, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142063, 63265, 2890, 'chrA07', 21988439, 'G', 'A', 964, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142064, 63265, 2908, 'chrA07', 21988457, 'G', 'C', 970, 'Asp', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01320); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142065, 63265, 2941, 'chrA07', 21988490, 'A', 'T', 981, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.31170); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142066, 63265, 2968, 'chrA07', 21988517, 'C', 'T', 990, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.02880); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142067, 63265, 3163, 'chrA07', 21988712, 'G', 'A', 1055, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.27470); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142068, 63265, 3188, 'chrA07', 21988737, 'C', 'G', 1063, 'Ala', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.27550); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142069, 63265, 3199, 'chrA07', 21988748, 'A', 'T', 1067, 'Ser', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.32070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142070, 63265, 3283, 'chrA07', 21988832, 'G', 'T', 1095, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142071, 63265, 3289, 'chrA07', 21988838, 'G', 'T', 1097, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327046, 1, 1319, 'chrC09', 9319194, 'G', 'A', 440, 'Ser', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327047, 1, 1085, 'chrC09', 9319428, 'C', 'T', 362, 'Arg', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327045, 2, 200, 'chrC09', 9311197, 'A', 'C', 67, 'His', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327036, 3, 385, 'chrC09', 9301658, 'T', 'A', 129, 'Phe', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327037, 3, 419, 'chrC09', 9301692, 'A', 'G', 140, 'Glu', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327038, 3, 726, 'chrC09', 9301999, 'C', 'G', 242, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327039, 3, 896, 'chrC09', 9302169, 'T', 'A', 299, 'Val', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00250); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327040, 3, 1106, 'chrC09', 9302379, 'G', 'T', 369, 'Arg', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00510); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327041, 3, 1220, 'chrC09', 9302493, 'A', 'T', 407, 'Glu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327042, 3, 1307, 'chrC09', 9302580, 'A', 'T', 436, 'His', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327043, 3, 1576, 'chrC09', 9302849, 'T', 'A', 526, 'Cys', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327044, 3, 1697, 'chrC09', 9302970, 'A', 'C', 566, 'Asn', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327035, 4, 67, 'chrC09', 9282013, 'C', 'A', 23, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327033, 5, 661, 'chrC09', 9273716, 'G', 'C', 221, 'Pro', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327034, 5, 481, 'chrC09', 9274017, 'A', 'T', 161, 'Leu', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327030, 6, 17, 'chrC09', 9267233, 'A', 'T', 6, 'Lys', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327031, 6, 305, 'chrC09', 9267521, 'G', 'C', 102, 'Gly', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327032, 6, 2093, 'chrC09', 9270136, 'G', 'T', 698, 'Gly', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327022, 7, 2450, 'chrC09', 9234630, 'G', 'T', 817, 'Ala', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00010); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327023, 7, 1718, 'chrC09', 9237814, 'A', 'C', 573, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00900); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327024, 7, 1408, 'chrC09', 9238193, 'T', 'C', 470, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327025, 7, 865, 'chrC09', 9238736, 'C', 'T', 289, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00200); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327026, 7, 825, 'chrC09', 9238776, 'G', 'T', 275, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.01230); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327027, 7, 763, 'chrC09', 9238838, 'A', 'G', 255, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327028, 7, 673, 'chrC09', 9238928, 'C', 'T', 225, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327029, 7, 612, 'chrC09', 9238989, 'A', 'T', 204, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327020, 8, 67, 'chrC09', 9230756, 'C', 'T', 23, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00350); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327021, 8, 81, 'chrC09', 9230770, 'G', 'C', 27, 'Glu', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.43170); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327018, 9, 169, 'chrC09', 9195157, 'T', 'C', 57, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00130); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327019, 9, 457, 'chrC09', 9195518, 'A', 'G', 153, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327014, 10, 191, 'chrC09', 9191243, 'G', 'A', 64, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.44000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327015, 10, 188, 'chrC09', 9191246, 'G', 'T', 63, 'Pro', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327016, 10, 164, 'chrC09', 9191270, 'C', 'T', 55, 'Arg', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.44160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327017, 10, 43, 'chrC09', 9191391, 'C', 'T', 15, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.43260); + + + + + + + +SET SQL_MODE=@OLD_SQL_MODE; +SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS; +SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS; + diff --git a/config/databases/homologs_db.sql b/config/databases/homologs_db.sql new file mode 100755 index 00000000..2f5e2ae0 --- /dev/null +++ b/config/databases/homologs_db.sql @@ -0,0 +1,120 @@ +SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO"; +START TRANSACTION; +SET time_zone = "+00:00"; +CREATE SCHEMA IF NOT EXISTS `homologs_db` DEFAULT CHARACTER SET utf8 ; +USE homologs_db; +DROP TABLE IF EXISTS `homologs_db`.`homologs` ; +CREATE TABLE `homologs` ( + `homologs_id` INT auto_increment, + `search_protein_name` varchar(45) NOT NULL, + `result_protein_name` varchar(45) NOT NULL, + `search_species_name` varchar(45) NOT NULL, + `result_species_name` varchar(45) NOT NULL, + `Percent_id` decimal(10, 5) NOT NULL, + `e_score` varchar(10) NOT NULL, + `is_search_structure` INT NOT NULL,/*1 represent has structure*/ + `is_result_structure` INT NOT NULL, + PRIMARY KEY (homologs_id) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; + + +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1, 'AT5G16970.1', 'BnaC09g40930D', 'arabidopsis', 'canola', 86.04700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (2, 'AT5G16970.1', 'BnaA10g17570D', 'arabidopsis', 'canola', 86.04700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (3, 'AT5G16970.1', 'BnaC03g08130D', 'arabidopsis', 'canola', 85.08800, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (4, 'AT5G16970.1', 'BnaA05g32330D', 'arabidopsis', 'canola', 81.63300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (5, 'AT5G16970.1', 'BnaCnng06210D', 'arabidopsis', 'canola', 80.87000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (6, 'AT5G16970.1', 'BnaA03g06330D', 'arabidopsis', 'canola', 85.37300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (7, 'AT5G16970.1', 'BnaA09g28840D', 'arabidopsis', 'canola', 77.90700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (8, 'AT5G16970.1', 'BnaC05g20410D', 'arabidopsis', 'canola', 77.32600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (9, 'AT5G16970.1', 'BnaC02g06960D', 'arabidopsis', 'canola', 76.23200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (10, 'AT5G16970.1', 'BnaA02g03340D', 'arabidopsis', 'canola', 75.94200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (11, 'AT4G32100.1', 'BnaC01g06360D', 'arabidopsis', 'canola', 55.28500, '2.18e-39'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (12, 'AT4G32100.1', 'BnaA01g04810D', 'arabidopsis', 'canola', 55.28500, '1.46e-38'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (13, 'AT4G32100.1', 'BnaA01g04820D', 'arabidopsis', 'canola', 52.84600, '6.47e-38'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (14, 'AT4G32100.1', 'BnaAnng05770D', 'arabidopsis', 'canola', 53.33300, '1.23e-37'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (15, 'AT4G32100.1', 'BnaC01g06960D', 'arabidopsis', 'canola', 51.61300, '1.19e-36'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (16, 'AT4G32100.1', 'BnaC07g18640D', 'arabidopsis', 'canola', 51.66700, '6.37e-36'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (17, 'AT4G32100.1', 'BnaA01g34870D', 'arabidopsis', 'canola', 49.19400, '4.15e-35'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (18, 'AT4G32100.1', 'BnaA02g24080D', 'arabidopsis', 'canola', 49.13800, '3.63e-27'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (19, 'AT4G32100.1', 'BnaA02g24090D', 'arabidopsis', 'canola', 48.27600, '6.69e-27'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (20, 'AT4G32100.1', 'BnaC02g31830D', 'arabidopsis', 'canola', 47.41400, '2.72e-25'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (21, 'AT2G43120.2', 'BnaC04g02730D', 'arabidopsis', 'canola', 90.96600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (22, 'AT2G43120.2', 'BnaC03g24040D', 'arabidopsis', 'canola', 91.27700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (23, 'AT2G43120.2', 'BnaA03g20050D', 'arabidopsis', 'canola', 90.65400, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824264, 'BnaC07g23540D', 'AT5G65470.1', 'canola', 'arabidopsis', 39.72900, '9.91e-109'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824265, 'BnaC07g23540D', 'AT4G24530.1', 'canola', 'arabidopsis', 36.96500, '1.03e-108'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824266, 'BnaC07g23540D', 'AT2G01480.1', 'canola', 'arabidopsis', 41.78400, '2.97e-107'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824267, 'BnaC07g23540D', 'AT2G01480.2', 'canola', 'arabidopsis', 43.07700, '6.19e-104'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824268, 'BnaC07g23540D', 'AT1G14970.2', 'canola', 'arabidopsis', 40.00000, '1.03e-103'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824269, 'BnaC07g23540D', 'AT1G14970.1', 'canola', 'arabidopsis', 40.00000, '2.33e-102'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824270, 'BnaC07g23540D', 'AT1G14970.3', 'canola', 'arabidopsis', 40.24700, '2.02e-101'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824271, 'BnaC07g23540D', 'AT1G38065.2', 'canola', 'arabidopsis', 39.86200, '2.00e-95'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824272, 'BnaC07g23550D', 'AT3G26400.1', 'canola', 'arabidopsis', 77.19600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824273, 'BnaC07g23550D', 'AT1G13020.1', 'canola', 'arabidopsis', 67.31400, '1.71e-180'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824274, 'BnaC07g23560D', 'AT3G26410.1', 'canola', 'arabidopsis', 93.21100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824275, 'BnaC07g23570D', 'AT3G26420.1', 'canola', 'arabidopsis', 79.75700, '1.69e-126'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824276, 'BnaC07g23570D', 'AT2G21660.1', 'canola', 'arabidopsis', 60.49400, '1.99e-30'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824277, 'BnaC07g23570D', 'AT4G39260.3', 'canola', 'arabidopsis', 57.31700, '6.84e-30'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824278, 'BnaC07g23570D', 'AT5G04280.1', 'canola', 'arabidopsis', 41.95100, '2.88e-29'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824279, 'BnaC07g23570D', 'AT4G39260.2', 'canola', 'arabidopsis', 58.02500, '4.78e-29'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824280, 'BnaC07g23570D', 'AT1G60650.2', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824281, 'BnaC07g23570D', 'AT1G60650.1', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824282, 'BnaC07g23570D', 'AT4G39260.4', 'canola', 'arabidopsis', 56.06100, '2.46e-21'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824283, 'BnaC07g23580D', 'AT3G26430.1', 'canola', 'arabidopsis', 84.21100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824284, 'BnaC07g23580D', 'AT1G67830.1', 'canola', 'arabidopsis', 60.58800, '2.97e-155'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824285, 'BnaC07g23580D', 'AT5G14450.1', 'canola', 'arabidopsis', 50.66000, '4.50e-131'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320148, 'BnaA10g09850D', 'BnaA10g09850D', 'canola', 'canola', 100.00000, '5.68e-110'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320149, 'BnaA10g09850D', 'BnaC09g32290D', 'canola', 'canola', 93.59000, '5.28e-93'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320150, 'BnaA10g09850D', 'BnaC02g12890D', 'canola', 'canola', 72.85700, '3.68e-26'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320151, 'BnaA10g09860D', 'BnaA10g09860D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320152, 'BnaA10g09860D', 'BnaC09g32300D', 'canola', 'canola', 86.68300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320153, 'BnaA10g09860D', 'BnaA02g08940D', 'canola', 'canola', 69.50900, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320154, 'BnaA10g09860D', 'BnaC02g12870D', 'canola', 'canola', 83.58500, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320155, 'BnaA10g09860D', 'BnaC08g12230D', 'canola', 'canola', 58.34400, '1.15e-177'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320156, 'BnaA10g09860D', 'BnaA01g15750D', 'canola', 'canola', 55.24900, '1.77e-162'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320157, 'BnaA10g09860D', 'BnaC01g18800D', 'canola', 'canola', 62.35600, '5.48e-116'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320158, 'BnaA10g09860D', 'BnaA06g19020D', 'canola', 'canola', 34.15200, '4.23e-50'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320159, 'BnaA10g09860D', 'BnaC09g05960D', 'canola', 'canola', 44.25500, '2.79e-46'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320160, 'BnaA10g09860D', 'BnaA06g22700D', 'canola', 'canola', 42.16900, '2.31e-43'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320161, 'BnaA10g09870D', 'BnaA10g09870D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320162, 'BnaA10g09870D', 'BnaC09g32310D', 'canola', 'canola', 90.82800, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320163, 'BnaA10g09870D', 'BnaA02g08930D', 'canola', 'canola', 72.72700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320164, 'BnaA10g09870D', 'BnaC02g12860D', 'canola', 'canola', 70.51700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320165, 'BnaA10g09870D', 'BnaA03g11280D', 'canola', 'canola', 70.32600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320166, 'BnaA10g09870D', 'BnaC03g71710D', 'canola', 'canola', 87.03700, '1.49e-113'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320167, 'BnaA10g09880D', 'BnaA10g09880D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320168, 'BnaA10g09880D', 'BnaC09g32320D', 'canola', 'canola', 98.12600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320169, 'BnaA10g09880D', 'BnaA02g08870D', 'canola', 'canola', 85.38300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320170, 'BnaA10g09880D', 'BnaA01g20560D', 'canola', 'canola', 51.22000, '1.02e-130'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320171, 'BnaA10g09880D', 'BnaC01g25850D', 'canola', 'canola', 51.81100, '9.19e-130'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320172, 'BnaA10g09880D', 'BnaA06g19130D', 'canola', 'canola', 51.24000, '4.00e-128'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690828, 'BnaA07g31480D', 'AT1G74360.1', 'canola', 'arabidopsis', 84.02200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690829, 'BnaA07g31480D', 'AT2G01950.1', 'canola', 'arabidopsis', 32.34200, '3.57e-149'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690830, 'BnaA07g31480D', 'AT1G55610.1', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690831, 'BnaA07g31480D', 'AT1G55610.2', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690832, 'BnaA07g31480D', 'AT1G17230.1', 'canola', 'arabidopsis', 32.44000, '7.99e-146'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690833, 'BnaA07g31480D', 'AT1G17230.2', 'canola', 'arabidopsis', 32.44000, '1.34e-145'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690834, 'BnaA07g31480D', 'AT4G39400.1', 'canola', 'arabidopsis', 33.15200, '5.71e-145'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690835, 'BnaA07g31480D', 'AT3G13380.1', 'canola', 'arabidopsis', 32.44600, '3.05e-143'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690836, 'BnaA07g31480D', 'AT5G63930.1', 'canola', 'arabidopsis', 33.05600, '1.84e-142'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690837, 'BnaA07g31480D', 'AT5G63930.2', 'canola', 'arabidopsis', 33.23900, '3.94e-141'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356296, 'BnaA07g31480D', 'BnaA07g31480D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356297, 'BnaA07g31480D', 'BnaC06g35270D', 'canola', 'canola', 96.79400, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356298, 'BnaA07g31480D', 'BnaCnng50590D', 'canola', 'canola', 75.29100, '5.45e-180'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356299, 'BnaA07g31480D', 'BnaA02g11590D', 'canola', 'canola', 74.41900, '3.01e-178'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356300, 'BnaA07g31480D', 'BnaC05g13410D', 'canola', 'canola', 32.51300, '7.21e-153'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356301, 'BnaA07g31480D', 'BnaA06g11580D', 'canola', 'canola', 33.08800, '1.36e-152'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356302, 'BnaA07g31480D', 'BnaC07g47240D', 'canola', 'canola', 33.42600, '6.47e-151'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356303, 'BnaA07g31480D', 'BnaA01g05490D', 'canola', 'canola', 33.58100, '3.69e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356304, 'BnaA07g31480D', 'BnaC07g21390D', 'canola', 'canola', 32.23900, '2.77e-147'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356305, 'BnaA07g31480D', 'BnaA06g34400D', 'canola', 'canola', 31.89600, '3.39e-147'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86750, 'AT1G74360.1', 'BnaC06g35270D', 'arabidopsis', 'canola', 84.27700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86751, 'AT1G74360.1', 'BnaA07g31480D', 'arabidopsis', 'canola', 84.02200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86752, 'AT1G74360.1', 'BnaA02g11590D', 'arabidopsis', 'canola', 77.97100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86753, 'AT1G74360.1', 'BnaCnng50590D', 'arabidopsis', 'canola', 77.97100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86754, 'AT1G74360.1', 'BnaA08g00410D', 'arabidopsis', 'canola', 31.84900, '5.39e-154'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86755, 'AT1G74360.1', 'BnaA06g11580D', 'arabidopsis', 'canola', 33.86600, '3.20e-153'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86756, 'AT1G74360.1', 'BnaA02g16780D', 'arabidopsis', 'canola', 67.03000, '2.11e-152'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86757, 'AT1G74360.1', 'BnaA06g34400D', 'arabidopsis', 'canola', 32.93200, '1.50e-151'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86758, 'AT1G74360.1', 'BnaA08g16520D', 'arabidopsis', 'canola', 33.89500, '1.68e-150'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86759, 'AT1G74360.1', 'BnaC07g47240D', 'arabidopsis', 'canola', 33.88700, '3.05e-150'); diff --git a/config/init.sh b/config/init.sh index 23bd482f..50b7f102 100755 --- a/config/init.sh +++ b/config/init.sh @@ -40,6 +40,8 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/striga.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql echo "Data are now loaded. Preparing API config" diff --git a/tests/data/get_canola_homolog_information.json b/tests/data/get_canola_homolog_information.json new file mode 100644 index 00000000..91e9fbb2 --- /dev/null +++ b/tests/data/get_canola_homolog_information.json @@ -0,0 +1,47 @@ +{ + "wasSuccessful": true, + "data": { + "homologs": [ + { + "search_species_name": "arabidoposis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC09g40930D", + "Percent_id": 86.047, + "e_score": 0 + }, + { + "search_species_name": "arabidoposis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA10g17570D", + "Percent_id": 86.047, + "e_score": 0 + }, + { + "search_species_name": "arabidoposis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC03g08130D", + "Percent_id": 85.088, + "e_score": 0 + }, + { + "search_species_name": "arabidoposis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA05g32330D", + "Percent_id": 81.633, + "e_score": 0 + }, + { + "search_species_name": "arabidoposis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaCnng06210D", + "Percent_id": 80.87, + "e_score": 0 + } + ] + } +} \ No newline at end of file diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index 61e6d4b7..c4f61aa5 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -1,6 +1,7 @@ from api import app from unittest import TestCase import pytest +from json import load class TestIntegrations(TestCase): @@ -95,6 +96,31 @@ def test_get_snps(self): } self.assertEqual(response.json, expected) + # Valid request canola + response = self.app_client.get("/snps/canola/BnaC09g12790D") + expected = { + "wasSuccessful": True, + "data": [ + [ + "chrC09", + 22, + None, + "missense_variant", + "MODERATE", + "MISSENSE", + "67C>A", + "ValPhe", + None, + "BnaC09g12790D", + "protein_coding", + "CODING", + "GSBRNA2T00000007001", + 0.0066 + ] + ] + } + self.assertEqual(response.json, expected) + # Invalid gene id response = self.app_client.get("/snps/poplar/abc") expected = {"wasSuccessful": False, "error": "Invalid gene id"} @@ -108,6 +134,19 @@ def test_get_snps(self): } self.assertEqual(response.json, expected) + # Invalid gene id for canola + response = self.app_client.get("/snps/canola/abc") + expected = {"wasSuccessful": False, "error": "Invalid gene id"} + self.assertEqual(response.json, expected) + + # Gene does not exist for canola + response = self.app_client.get("/snps/poplar/BnaC09g99999D") + expected = { + "wasSuccessful": False, + "error": "There are no data found for the given gene", + } + self.assertEqual(response.json, expected) + def test_get_sample_definitions(self): """ Test cases for sample definition @@ -218,3 +257,41 @@ def test_pymol_snps_pymol_unneeded(self): response = self.app_client.get("/snps/pymol/Potri.016G107900.1?snps=25l&chain=None") expected = {"wasSuccessful": False, "error": "Invalid SNP string format"} self.assertEqual(response.json, expected) + + def test_homologs(self): + + # test for get homologs + response = self.app_client.get("/snps/homologs/arabidopsis/AT5G16970.1/canola") + with open("tests/data/get_canola_homolog_information.json") as file: + expected = load(file) + self.assertEqual(response.json, expected) + + # test for invalid input + response = self.app_client.get("/snps/homologs/rice/AT3G18710.1/canola") + expected = { + "wasSuccessful": False, + "error": "Species not supported", + } + self.assertEqual(response.json, expected) + + response = self.app_client.get("/snps/homologs/arabidopsis/AT3G18710.1/rice") + expected = { + "wasSuccessful": False, + "error": "Species not supported", + } + self.assertEqual(response.json, expected) + + response = self.app_client.get("/snps/homologs/arabidopsis/abc/canola") + expected = { + "wasSuccessful": False, + "error": "Invalid gene id", + } + self.assertEqual(response.json, expected) + + # test for no homologs data + response = self.app_client.get("/snps/homologs/arabidopsis/AT3G18710.1/canola") + expected = { + "wasSuccessful": False, + "error": "No homologs found for the given query", + } + self.assertEqual(response.json, expected) \ No newline at end of file From c2f39113c769d52b76d1e35057bd162d1d19e0da Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 22 Mar 2025 16:20:36 -0400 Subject: [PATCH 03/14] Add Support of SNP query of Canola and add new endpoint for Homolog query (only support Arabidopsis and Brassica napus now) --- .../data/get_canola_homolog_information.json | 90 +++++++++---------- 1 file changed, 45 insertions(+), 45 deletions(-) diff --git a/tests/data/get_canola_homolog_information.json b/tests/data/get_canola_homolog_information.json index 91e9fbb2..3a6cb8a8 100644 --- a/tests/data/get_canola_homolog_information.json +++ b/tests/data/get_canola_homolog_information.json @@ -1,47 +1,47 @@ { - "wasSuccessful": true, - "data": { - "homologs": [ - { - "search_species_name": "arabidoposis", - "search_protein_name": "AT5G16970.1", - "result_species_name": "canola", - "result_protein_name": "BnaC09g40930D", - "Percent_id": 86.047, - "e_score": 0 - }, - { - "search_species_name": "arabidoposis", - "search_protein_name": "AT5G16970.1", - "result_species_name": "canola", - "result_protein_name": "BnaA10g17570D", - "Percent_id": 86.047, - "e_score": 0 - }, - { - "search_species_name": "arabidoposis", - "search_protein_name": "AT5G16970.1", - "result_species_name": "canola", - "result_protein_name": "BnaC03g08130D", - "Percent_id": 85.088, - "e_score": 0 - }, - { - "search_species_name": "arabidoposis", - "search_protein_name": "AT5G16970.1", - "result_species_name": "canola", - "result_protein_name": "BnaA05g32330D", - "Percent_id": 81.633, - "e_score": 0 - }, - { - "search_species_name": "arabidoposis", - "search_protein_name": "AT5G16970.1", - "result_species_name": "canola", - "result_protein_name": "BnaCnng06210D", - "Percent_id": 80.87, - "e_score": 0 - } - ] - } + "wasSuccessful": true, + "data": { + "homologs": [ + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC09g40930D", + "Percent_id": 86.047, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA10g17570D", + "Percent_id": 86.047, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC03g08130D", + "Percent_id": 85.088, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA05g32330D", + "Percent_id": 81.633, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaCnng06210D", + "Percent_id": 80.87, + "e_score": 0.0 + } + ] + } } \ No newline at end of file From e587ce779e4ba3dc3b75c8a35dabebbfe79a702c Mon Sep 17 00:00:00 2001 From: Asher Date: Fri, 28 Mar 2025 17:53:39 -0400 Subject: [PATCH 04/14] =?UTF-8?q?Revert=20"mfinder=20second=20commit,=20mo?= =?UTF-8?q?st=20functions=20moved=20to=20util=20file.=20Modified=20in?= =?UTF-8?q?=E2=80=A6"?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- api/resources/interactions.py | 26 +--- api/utils/mfinder_utils.py | 200 --------------------------- tests/resources/test_interactions.py | 55 -------- 3 files changed, 1 insertion(+), 280 deletions(-) delete mode 100644 api/utils/mfinder_utils.py diff --git a/api/resources/interactions.py b/api/resources/interactions.py index 7fa2c9e9..81688760 100644 --- a/api/resources/interactions.py +++ b/api/resources/interactions.py @@ -5,10 +5,9 @@ """ from flask_restx import Namespace, Resource, fields -from flask import request, jsonify +from flask import request from markupsafe import escape from api.utils.bar_utils import BARUtils -from api.utils.mfinder_utils import MfinderUtils from marshmallow import Schema, ValidationError, fields as marshmallow_fields from api import db from api.models.rice_interactions import Interactions as RiceInteractions @@ -157,26 +156,3 @@ def post(self): return BARUtils.success_exit(res) else: return BARUtils.error_exit("No data for the given species/genes"), 400 - - -@itrns.route("/mfinder") -class MFinder(Resource): - @itrns.expect(post_int_data) - def post(self): - """This endpoint was originally written by Vincent Lau to return mFinder - results to AGENT in his express node.JS app. However Tianhui Zhao refactored - to the BAR_API - """ - data = request.get_json() - # Validate json - try: - data = MFinderDataSchema().load(data) - except ValidationError as err: - return BARUtils.error_exit(err.messages), 400 - - filtered_valid_arr = MfinderUtils.input_validation(data["data"]) - if isinstance(filtered_valid_arr, str): - return BARUtils.error_exit(filtered_valid_arr), 400 - settings = MfinderUtils.settings_validation(data.get("options", {})) - ret_json = MfinderUtils.create_files_and_mfinder(filtered_valid_arr, settings) - return jsonify(MfinderUtils.beautify_results(ret_json)) diff --git a/api/utils/mfinder_utils.py b/api/utils/mfinder_utils.py deleted file mode 100644 index 46d517d7..00000000 --- a/api/utils/mfinder_utils.py +++ /dev/null @@ -1,200 +0,0 @@ -from api.utils.bar_utils import BARUtils - -import tempfile -import os -import subprocess -from collections import defaultdict - - -class MfinderUtils: - - @staticmethod - # Eliminates same pairs - def uniq_with(arr, comp_func): - unique_arr = [] - for item in arr: - if not any(comp_func(item, unique_item) for unique_item in unique_arr): - unique_arr.append(item) - return unique_arr - - @staticmethod - def is_equal(a, b): - return a == b - - @staticmethod - def find_key(d, value): - return next(key for key, val in d.items() if val == value) - - # Check if JSON body data obj is an array of arrays (2d arr) - # ex [ [ "AT1G010100", "AT5G01010" ], ["AT3G10000", "AT2G03240"]] - # {Array>} input: the above arr - @staticmethod - def input_validation(input): - if not isinstance(input, list): - return "invalid JSON, not an arr" - - if len(input) == 0: - return "arr length 0!" - - if any(len(i) != 2 for i in input): - return "inner arr length is not of length 2!" - - if not all(isinstance(i, list) for i in input): - return "invalid JSON, check arr members are arrs!" - - if not all(isinstance(j, str) for i in input for j in i): - return "invalid JSON, check if inside arr members are strings!" - - if not all(BARUtils.is_arabidopsis_gene_valid(j) for i in input for j in i): - return "Invalid gene ID contained!" - - # filter self-edges and duplicate edges (mFinder does not accept) - return MfinderUtils.uniq_with([i for i in input if i[0] != i[1]], MfinderUtils.is_equal) - - # Some mFinders params allowed within reasonable server load. Namely mFinder takes 3 basic params: nd (non-directed network), - # r (# of rand networks to gen), s (motif size), u (unique min), z (z-score min). The defaults are directed, 100, 3, 4, & 2 - # respectively. HOWEVER choose r of 30 for speed - # Do a validation check on each value too! - # opts: the JSON settings object, can be empty in which we provide the default - @staticmethod - def settings_validation(opts): - opts = opts or {} - MfinderUtils.injection_check(opts) - settings_obj = opts.copy() - if "nd" not in opts: - settings_obj["nd"] = False - elif not isinstance(opts["nd"], bool): - return "incorrect nd setting - is it boolean?", 400 - - if "r" not in opts: - settings_obj["r"] = 50 - elif not isinstance(opts["r"], int) or opts["r"] > 150: - return "incorrect r setting - is it a number under 151?", 400 - - if "s" not in opts: - settings_obj["s"] = 3 - elif not isinstance(opts["s"], int) or opts["s"] < 2 or opts["s"] > 4: - return "incorrect s setting - is it a number between 2 and 4?", 400 - - if "u" not in opts: - settings_obj["u"] = 4 - elif not isinstance(opts["u"], int) or opts["u"] > 999: - return "incorrect u setting - is it a number or below 1000?", 400 - - if "z" not in opts: - settings_obj["z"] = 2 - elif not isinstance(opts["z"], int) or opts["z"] > 99: - return "incorrect z setting - is it a number or below 100?", 400 - - return settings_obj - - # Check for injection, throw if suspiciously long command is found. - # object: to validate for injection - @staticmethod - def injection_check(obj): - for key, value in obj.items(): - if len(str(value)) > 10: - return f"{key} settings param is too long", 400 - - # Take in the filtered array of gene-id pairs (edges) and perform - # mFinder analysis on them (create temp text files to do so) - # Performed SYNCHRONOUSLY !!! - @staticmethod - def create_files_and_mfinder(input, opts_obj): - - # give read/write permissions to user but nada to anybody else - tmpfile = tempfile.NamedTemporaryFile(mode="w+", suffix=".txt", delete=False) - os.chmod(tmpfile.name, 0o600) - - # get a hash of IDs -> numbers for later lookup and writable string - hash_of_ids, return_str = MfinderUtils.get_gene_id_hash_map(input) - - # write to temp file which mFinder will run/read on - tmpfile.write(return_str) - tmpfile.flush() - - # file_path = "/usr/src/app/mfinder/mfinder1.21_1/mfinder" - - # if os.access(file_path, os.X_OK): - # return (f"The file exists {tmpfile.name}") - # else: - # return "The file does not exist" - - command = ( - f"/bartmp/mfinder {tmpfile.name} " - f"-s {opts_obj['s']} " - f"-r {opts_obj['r']} " - f"-u {opts_obj['u']} " - f"-z {opts_obj['z']} " - f"{'-nd ' if opts_obj.get('nd') else ''}" - "-omem" - ) - subprocess.run(command, shell=True, check=True) - - with open(tmpfile.name[:-4] + "_OUT.txt", "r") as stats_file: - mfinder_stats = stats_file.read() - - with open(tmpfile.name[:-4] + "_MEMBERS.txt", "r") as members_file: - mfinder_members = members_file.read() - - tmpfile.close() - print(f"Temporary file: {tmpfile.name}") - os.remove(tmpfile.name) - - return {"hashOfIds": hash_of_ids, "mFinderStats": mfinder_stats, "mFinderMembers": mfinder_members} - - # Take an input of array of array of strings which represent edges and transform those gene IDs (unique!) to a hash table and - # coinciding edges i.e. [["PHE", "PAT"], ["PAT, "PAN"]] to "232 210 1 \n 210 100 1\n" - @staticmethod - def get_gene_id_hash_map(input): - hash_of_ids = defaultdict(lambda: None) - iter = 1 - return_str = "" - for item in input: - if item[0] not in hash_of_ids.values(): - hash_of_ids[iter] = item[0] - iter += 1 - if item[1] not in hash_of_ids.values(): - hash_of_ids[iter] = item[1] - iter += 1 - return_str += f"{MfinderUtils.find_key(hash_of_ids, item[0])} {MfinderUtils.find_key(hash_of_ids, item[1])} 1\n" - - return hash_of_ids, return_str - - # Beautify the output file string and members file string - @staticmethod - def beautify_results(mfinder_res_obj): - stats = mfinder_res_obj["mFinderStats"] - mems = mfinder_res_obj["mFinderMembers"] - id_map = mfinder_res_obj["hashOfIds"] - ret_obj = {"sigMotifs": {}, "motifList": {}} - - try: - sig_motifs_str = stats.split("[MILI]\t\n\n")[1].split("Full")[0].split("\n\n") - # In case stats has less than 2 parts after split('[MILI]\t\n\n')[1] - except IndexError: - raise ValueError("Expected delimiter '[MILI]\t\n\n' or 'Full' not found in the stats string.") - sig_motifs_str = sig_motifs_str[: len(sig_motifs_str) - 2 : 2] - for item in sig_motifs_str: - split_stats_for_motif_id = item.split("\t") - ret_obj["sigMotifs"][split_stats_for_motif_id[0]] = { - "numAppearances": split_stats_for_motif_id[1], - "numAppearancesRand": split_stats_for_motif_id[2], - "appearancesZScore": split_stats_for_motif_id[3], - "pValue": split_stats_for_motif_id[4], - "uniq": split_stats_for_motif_id[5], - "conc": split_stats_for_motif_id[6], - } - - subgraphs_list_str = mems.split("subgraph id = ")[1:] - for subgraph_str in subgraphs_list_str: - member_list_split = subgraph_str.split("\n") - motif_mem_list = [i.rstrip("\t") for i in member_list_split[5:-2]] - motif_mem_results = [] - for i in motif_mem_list: - three_genes = i.split("\t") - formatted_str = f"{id_map[int(three_genes[0])]}\t{id_map[int(three_genes[1])]}\t{id_map[int(three_genes[2])]}" # i.e. PAT\tPAN\tEGFR - motif_mem_results.append(formatted_str) - ret_obj["motifList"][member_list_split[0]] = motif_mem_results - - return BARUtils.success_exit(ret_obj) diff --git a/tests/resources/test_interactions.py b/tests/resources/test_interactions.py index fdb3a2b8..3f089b41 100644 --- a/tests/resources/test_interactions.py +++ b/tests/resources/test_interactions.py @@ -1,7 +1,6 @@ from api import app from unittest import TestCase import json -from json import load class TestIntegrations(TestCase): @@ -132,57 +131,3 @@ def test_post_itrns(self): "error": "No data for the given species/genes", } self.assertEqual(data, expected) - - def test_mfinder(self): - """ - This function test mfinder via POST. - """ - # Valid request - with open("tests/data/mfinder_input.json") as json_file_1: - input_data = load(json_file_1) - response = self.app_client.post( - "/interactions/mfinder", - json=input_data, - ) - data = json.loads(response.get_data(as_text=True)) - with open("tests/data/mfinder_output.json") as json_file_2: - expected = load(json_file_2) - self.assertEqual(data, expected) - - # Invalid data structure - response = self.app_client.post("/interactions/mfinder", json={"data": {}}) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": {"data": ["Not a valid list."]}} - self.assertEqual(data, expected) - - response = self.app_client.post("/interactions/mfinder", json={"data": []}) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": "arr length 0!"} - self.assertEqual(data, expected) - - response = self.app_client.post( - "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420"]]} - ) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": "inner arr length is not of length 2!"} - self.assertEqual(data, expected) - - response = self.app_client.post("/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], 1]}) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": {"data": {"1": ["Not a valid list."]}}} - self.assertEqual(data, expected) - - response = self.app_client.post( - "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420", 1]]} - ) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": {"data": {"1": {"1": ["Not a valid string."]}}}} - self.assertEqual(data, expected) - - # Invalid gene ID - response = self.app_client.post( - "/interactions/mfinder", json={"data": [["AT1G01010", "AT5G01010"], ["001G01030", "AT2G03240"]]} - ) - data = json.loads(response.get_data(as_text=True)) - expected = {"wasSuccessful": False, "error": "Invalid gene ID contained!"} - self.assertEqual(data, expected) From 01cc40d3cf436f6c1de27003eed13d5cac35b3e7 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 15:17:21 -0400 Subject: [PATCH 05/14] fix typo --- api/models/canola_nssnp.py | 5 +++-- api/models/homologs_db.py | 2 +- api/resources/snps.py | 10 +++------- 3 files changed, 7 insertions(+), 10 deletions(-) diff --git a/api/models/canola_nssnp.py b/api/models/canola_nssnp.py index ac63582e..2c3fb2b3 100755 --- a/api/models/canola_nssnp.py +++ b/api/models/canola_nssnp.py @@ -1,8 +1,9 @@ from typing import Optional from api import db -#from sqlalchemy.ext.declarative import declarative_base +# from sqlalchemy.ext.declarative import declarative_base -#CanolaBase = declarative_base() + +# CanolaBase = declarative_base() class CanolaProteinReference(db.Model): __bind_key__ = "canola_nssnp" __tablename__ = "protein_reference" diff --git a/api/models/homologs_db.py b/api/models/homologs_db.py index 7b0d985d..a6f87a87 100644 --- a/api/models/homologs_db.py +++ b/api/models/homologs_db.py @@ -10,5 +10,5 @@ class homologs(db.Model): result_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) search_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) result_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) - Percent_id: db.Mapped[float] = db.mapped_column(db.Numeric(10,5), nullable=False) + Percent_id: db.Mapped[float] = db.mapped_column(db.Numeric(10, 5), nullable=False) e_score: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False) diff --git a/api/resources/snps.py b/api/resources/snps.py index 721943bd..ddc12cf0 100755 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -543,7 +543,7 @@ def get(self, pval="", araid="", popid=""): @snps.route("/homologs///") -class SeqHotspots(Resource): +class Homologs(Resource): @snps.param("search_species", _in="path", default="canola") @snps.param("search_gene", _in="path", default="BnaA07g31480D") @snps.param("target_species", _in="path", default="arabidopsis") @@ -559,8 +559,7 @@ def get(self, search_species="", search_gene="", target_species=""): supported = ["arabidopsis", "canola"] if (search_species not in supported) or (target_species not in supported): return BARUtils.error_exit("Species not supported"), 400 - elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or \ - (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)): + elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)): results = HomologsDB.query.filter_by( search_protein_name=gene_id, search_species_name=search_species, @@ -582,10 +581,7 @@ def get(self, search_species="", search_gene="", target_species=""): ] homologs_list.sort(key=lambda x: x["e_score"]) if len(homologs_list) >= 5: homologs_list = homologs_list[:5] - response = { - "homologs": homologs_list - } - + response = {"homologs": homologs_list} return BARUtils.success_exit(response), 200 else: return BARUtils.error_exit("Invalid gene id"), 400 From ab6792a9b46c59b5640a1bdf795aff260259fa08 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 15:20:15 -0400 Subject: [PATCH 06/14] fix typo --- api/resources/snps.py | 5 ++--- tests/resources/test_snps.py | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/api/resources/snps.py b/api/resources/snps.py index ddc12cf0..038b2675 100755 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -580,10 +580,9 @@ def get(self, search_species="", search_gene="", target_species=""): for homolog in results ] homologs_list.sort(key=lambda x: x["e_score"]) - if len(homologs_list) >= 5: homologs_list = homologs_list[:5] + if len(homologs_list) >= 5: + homologs_list = homologs_list[:5] response = {"homologs": homologs_list} return BARUtils.success_exit(response), 200 else: return BARUtils.error_exit("Invalid gene id"), 400 - - diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index c4f61aa5..dd2296c4 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -294,4 +294,4 @@ def test_homologs(self): "wasSuccessful": False, "error": "No homologs found for the given query", } - self.assertEqual(response.json, expected) \ No newline at end of file + self.assertEqual(response.json, expected) From 56b60462de1f5653bb05e62faeb7642685d5287a Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 15:24:53 -0400 Subject: [PATCH 07/14] fix typo --- api/utils/bar_utils.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index 3dd6cfa1..b4f6a492 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -83,6 +83,17 @@ def is_cannabis_gene_valid(gene): else: return False + @staticmethod + def is_canola_gene_valid(gene): + """This function verifies if canola gene (BnaC07g42830D) is valid + :param gene: + :return: + """ + if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I): + return True + else: + return False + @staticmethod def is_arachis_gene_valid(gene): """This function verifies if arachis gene is valid: Adur10000_comp0_c0_seq1 From c291b5e21ede4a40605f82fd54d3acda5a217001 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 15:30:17 -0400 Subject: [PATCH 08/14] fix typo --- tests/resources/test_snps.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index dd2296c4..c53156ca 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -140,7 +140,7 @@ def test_get_snps(self): self.assertEqual(response.json, expected) # Gene does not exist for canola - response = self.app_client.get("/snps/poplar/BnaC09g99999D") + response = self.app_client.get("/snps/canola/BnaC07g99930D") expected = { "wasSuccessful": False, "error": "There are no data found for the given gene", From 17aa094e0fa0203e34e5b542de93e4a8b712bcc9 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 15:34:58 -0400 Subject: [PATCH 09/14] fix typo --- config/BAR_API.cfg | 1 + 1 file changed, 1 insertion(+) diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index 5210e706..71363b11 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -40,6 +40,7 @@ SQLALCHEMY_BINDS = { 'striga' : 'mysql://root:root@localhost/striga', 'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp', 'tomato_sequence' : 'mysql://root:root@localhost/tomato_sequence', + 'triphysaria' : 'mysql://root:root@localhost/triphysaria', 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', 'homologs_db' : 'mysql://root:root@localhost/homologs_db' From bf5377374a1fc6db64dedad5047f697c182c37b9 Mon Sep 17 00:00:00 2001 From: lixiaof8 Date: Sat, 29 Mar 2025 16:22:25 -0400 Subject: [PATCH 10/14] fix typo --- tests/data/get_canola_homolog_information.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/data/get_canola_homolog_information.json b/tests/data/get_canola_homolog_information.json index 3a6cb8a8..e11763cb 100644 --- a/tests/data/get_canola_homolog_information.json +++ b/tests/data/get_canola_homolog_information.json @@ -44,4 +44,4 @@ } ] } -} \ No newline at end of file +} From 74acf9de75da97e580899cfa62fb6de78fb9b770 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 29 Mar 2025 19:35:31 -0400 Subject: [PATCH 11/14] Minor changes. --- api/models/canola_nssnp.py | 1 - api/models/homologs_db.py | 2 +- api/resources/snps.py | 13 +- api/utils/bar_utils.py | 6 +- api/utils/docking_utils.py | 0 config/BAR_API.cfg | 7 +- config/databases/canola_nssnp.sql | 281 +++++++++++------------------- config/databases/homologs_db.sql | 180 +++++++------------ config/init.sh | 5 +- requirements.txt | 36 ++-- tests/resources/test_snps.py | 4 +- 11 files changed, 197 insertions(+), 338 deletions(-) mode change 100755 => 100644 api/models/canola_nssnp.py mode change 100755 => 100644 api/resources/snps.py mode change 100755 => 100644 api/utils/docking_utils.py mode change 100755 => 100644 config/databases/canola_nssnp.sql mode change 100755 => 100644 config/databases/homologs_db.sql diff --git a/api/models/canola_nssnp.py b/api/models/canola_nssnp.py old mode 100755 new mode 100644 index 2c3fb2b3..187ed42a --- a/api/models/canola_nssnp.py +++ b/api/models/canola_nssnp.py @@ -1,6 +1,5 @@ from typing import Optional from api import db -# from sqlalchemy.ext.declarative import declarative_base # CanolaBase = declarative_base() diff --git a/api/models/homologs_db.py b/api/models/homologs_db.py index a6f87a87..426d9b13 100644 --- a/api/models/homologs_db.py +++ b/api/models/homologs_db.py @@ -3,7 +3,7 @@ class homologs(db.Model): __bind_key__ = "homologs_db" - __tablename__ = 'homologs' + __tablename__ = "homologs" homologs_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) search_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) diff --git a/api/resources/snps.py b/api/resources/snps.py old mode 100755 new mode 100644 index 038b2675..b026b737 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -19,7 +19,7 @@ ) from api.models.canola_nssnp import ( CanolaProteinReference as CanolaProteinReference, - CanolaSnpsToProtein as CanolaSnpsToProtein + CanolaSnpsToProtein as CanolaSnpsToProtein, ) from api.models.homologs_db import homologs as HomologsDB from api.utils.bar_utils import BARUtils @@ -557,13 +557,14 @@ def get(self, search_species="", search_gene="", target_species=""): gene_id = escape(search_gene) target_species = escape(target_species) supported = ["arabidopsis", "canola"] + if (search_species not in supported) or (target_species not in supported): return BARUtils.error_exit("Species not supported"), 400 - elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)): + elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or ( + search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id) + ): results = HomologsDB.query.filter_by( - search_protein_name=gene_id, - search_species_name=search_species, - result_species_name=target_species + search_protein_name=gene_id, search_species_name=search_species, result_species_name=target_species ).all() if not results: return BARUtils.error_exit("No homologs found for the given query"), 400 @@ -575,7 +576,7 @@ def get(self, search_species="", search_gene="", target_species=""): "result_species_name": target_species, "result_protein_name": homolog.result_protein_name, "Percent_id": float(homolog.Percent_id), - "e_score": float(homolog.e_score) + "e_score": float(homolog.e_score), } for homolog in results ] diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index b4f6a492..7fe07391 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -86,9 +86,9 @@ def is_cannabis_gene_valid(gene): @staticmethod def is_canola_gene_valid(gene): """This function verifies if canola gene (BnaC07g42830D) is valid - :param gene: - :return: - """ + :param gene: + :return: + """ if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I): return True else: diff --git a/api/utils/docking_utils.py b/api/utils/docking_utils.py old mode 100755 new mode 100644 diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index 71363b11..f05a5fe9 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -15,6 +15,7 @@ SQLALCHEMY_BINDS = { 'arachis': 'mysql://root:root@localhost/arachis', 'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa', 'cannabis': 'mysql://root:root@localhost/cannabis', + 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', 'dna_damage': 'mysql://root:root@localhost/dna_damage', 'embryo': 'mysql://root:root@localhost/embryo', 'eplant2': 'mysql://root:root@localhost/eplant2', @@ -24,6 +25,7 @@ SQLALCHEMY_BINDS = { 'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato', 'fastpheno' : 'mysql://root:root@localhost/fastpheno', 'germination': 'mysql://root:root@localhost/germination', + 'homologs_db' : 'mysql://root:root@localhost/homologs_db', 'kalanchoe': 'mysql://root:root@localhost/kalanchoe', 'klepikova': 'mysql://root:root@localhost/klepikova', 'llama3': 'mysql://root:root@localhost/llama3', @@ -40,8 +42,5 @@ SQLALCHEMY_BINDS = { 'striga' : 'mysql://root:root@localhost/striga', 'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp', 'tomato_sequence' : 'mysql://root:root@localhost/tomato_sequence', - 'triphysaria' : 'mysql://root:root@localhost/triphysaria', - 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', - 'homologs_db' : 'mysql://root:root@localhost/homologs_db' - + 'triphysaria' : 'mysql://root:root@localhost/triphysaria' } diff --git a/config/databases/canola_nssnp.sql b/config/databases/canola_nssnp.sql old mode 100755 new mode 100644 index a89d10dd..46f1cb81 --- a/config/databases/canola_nssnp.sql +++ b/config/databases/canola_nssnp.sql @@ -1,183 +1,98 @@ -SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0; -SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0; -SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION'; - --- ----------------------------------------------------- --- Schema nov24_canola_snps --- ----------------------------------------------------- -DROP SCHEMA IF EXISTS `canola_nssnp` ; - --- ----------------------------------------------------- --- Schema nov24_canola_snps --- ----------------------------------------------------- -CREATE SCHEMA IF NOT EXISTS `canola_nssnp` DEFAULT CHARACTER SET utf8 ; -USE `canola_nssnp` ; - --- ----------------------------------------------------- --- Table `canola_nssnp`.`protein_reference` --- ----------------------------------------------------- -DROP TABLE IF EXISTS `canola_nssnp`.`protein_reference` ; - -create table protein_reference -( - protein_reference_id int auto_increment - primary key, - gene_identifier varchar(45) not null, - gene_name varchar(45) null -); - --- ----------------------------------------------------- --- Table `canola_nssnp`.`snps_to_protein` --- ----------------------------------------------------- -DROP TABLE IF EXISTS `canola_nssnp`.`snps_to_protein` ; - -create table snps_to_protein -( - snps_reference_id int auto_increment, - protein_reference_id int not null, - transcript_pos int not null, - chromosome varchar(25) not null, - chromosomal_loci int not null, - ref_DNA varchar(1) not null, - alt_DNA varchar(45) not null, - aa_pos int not null, - ref_aa varchar(3) not null, - alt_aa varchar(3) not null, - type varchar(50) not null, - effect_impact varchar(50) not null, - transcript_biotype varchar(45) null, - alt_freq decimal(10, 5) not null, - primary key (snps_reference_id, protein_reference_id), - constraint protein_fk - foreign key (protein_reference_id) references protein_reference (protein_reference_id) -); - -create index protein_fk_idx - on snps_to_protein (protein_reference_id); - - -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (1, 'GSBRNA2T00000001001', 'BnaC09g12820D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (2, 'GSBRNA2T00000003001', 'BnaC09g12810D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (3, 'GSBRNA2T00000005001', 'BnaC09g12800D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (4, 'GSBRNA2T00000007001', 'BnaC09g12790D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (5, 'GSBRNA2T00000008001', 'BnaC09g12780D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (6, 'GSBRNA2T00000009001', 'BnaC09g12770D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (7, 'GSBRNA2T00000011001', 'BnaC09g12760D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (8, 'GSBRNA2T00000012001', 'BnaC09g12750D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (9, 'GSBRNA2T00000015001', 'BnaC09g12740D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (10, 'GSBRNA2T00000016001', 'BnaC09g12730D'); -INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (63265, 'GSBRNA2T00102721001', 'BnaA07g31480D'); - -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142004, 63265, 52, 'chrA07', 21985117, 'A', 'C', 18, 'Met', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142005, 63265, 130, 'chrA07', 21985679, 'G', 'T', 44, 'Gly', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.04930); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142006, 63265, 163, 'chrA07', 21985712, 'C', 'G', 55, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.09210); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142007, 63265, 268, 'chrA07', 21985817, 'G', 'A', 90, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142008, 63265, 284, 'chrA07', 21985833, 'G', 'C', 95, 'Arg', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142009, 63265, 433, 'chrA07', 21985982, 'C', 'T', 145, 'Pro', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142010, 63265, 442, 'chrA07', 21985991, 'G', 'A', 148, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142011, 63265, 445, 'chrA07', 21985994, 'A', 'G', 149, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142012, 63265, 486, 'chrA07', 21986035, 'C', 'G', 162, 'His', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.08310); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142013, 63265, 500, 'chrA07', 21986049, 'T', 'G', 167, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08140); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142014, 63265, 526, 'chrA07', 21986075, 'G', 'A', 176, 'Gly', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08390); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142015, 63265, 541, 'chrA07', 21986090, 'T', 'C', 181, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142016, 63265, 634, 'chrA07', 21986183, 'C', 'A', 212, 'Leu', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142017, 63265, 640, 'chrA07', 21986189, 'C', 'T', 214, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142018, 63265, 694, 'chrA07', 21986243, 'G', 'T', 232, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142019, 63265, 769, 'chrA07', 21986318, 'T', 'C', 257, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.05180); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142020, 63265, 848, 'chrA07', 21986397, 'G', 'A', 283, 'Ser', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.05100); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142021, 63265, 859, 'chrA07', 21986408, 'T', 'C', 287, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.05920); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142022, 63265, 889, 'chrA07', 21986438, 'A', 'G', 297, 'Lys', 'Glu', 'missense_variant', 'MODERATE', 'protein_coding', 0.06330); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142023, 63265, 979, 'chrA07', 21986528, 'C', 'G', 327, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142024, 63265, 995, 'chrA07', 21986544, 'C', 'T', 332, 'Thr', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142025, 63265, 1039, 'chrA07', 21986588, 'C', 'T', 347, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.07070); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142026, 63265, 1042, 'chrA07', 21986591, 'T', 'C', 348, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142027, 63265, 1060, 'chrA07', 21986609, 'A', 'G', 354, 'Asn', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142028, 63265, 1075, 'chrA07', 21986624, 'T', 'C', 359, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142029, 63265, 1267, 'chrA07', 21986816, 'C', 'G', 423, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.07240); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142030, 63265, 1336, 'chrA07', 21986885, 'C', 'G', 446, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142031, 63265, 1363, 'chrA07', 21986912, 'G', 'A', 455, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.32150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142032, 63265, 1420, 'chrA07', 21986969, 'T', 'A', 474, 'Ser', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01810); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142033, 63265, 1462, 'chrA07', 21987011, 'C', 'G', 488, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.04610); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142034, 63265, 1595, 'chrA07', 21987144, 'A', 'C', 532, 'Glu', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.04440); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142035, 63265, 1735, 'chrA07', 21987284, 'C', 'G', 579, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.29930); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142036, 63265, 1744, 'chrA07', 21987293, 'T', 'C', 582, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.02380); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142037, 63265, 1865, 'chrA07', 21987414, 'C', 'T', 622, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142038, 63265, 2077, 'chrA07', 21987626, 'C', 'G', 693, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142039, 63265, 2086, 'chrA07', 21987635, 'C', 'A', 696, 'His', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142040, 63265, 2089, 'chrA07', 21987638, 'A', 'G', 697, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142041, 63265, 2215, 'chrA07', 21987764, 'A', 'T', 739, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142042, 63265, 2227, 'chrA07', 21987776, 'G', 'C', 743, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142043, 63265, 2233, 'chrA07', 21987782, 'T', 'C', 745, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142044, 63265, 2254, 'chrA07', 21987803, 'C', 'T', 752, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142045, 63265, 2323, 'chrA07', 21987872, 'T', 'C', 775, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.28040); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142046, 63265, 2350, 'chrA07', 21987899, 'G', 'A', 784, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142047, 63265, 2395, 'chrA07', 21987944, 'C', 'G', 799, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142048, 63265, 2425, 'chrA07', 21987974, 'G', 'C', 809, 'Val', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142049, 63265, 2434, 'chrA07', 21987983, 'A', 'G', 812, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142050, 63265, 2446, 'chrA07', 21987995, 'A', 'G', 816, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142051, 63265, 2464, 'chrA07', 21988013, 'A', 'C', 822, 'Ser', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27140); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142052, 63265, 2518, 'chrA07', 21988067, 'C', 'G', 840, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142053, 63265, 2521, 'chrA07', 21988070, 'T', 'G', 841, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.24180); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142054, 63265, 2545, 'chrA07', 21988094, 'G', 'A', 849, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.31830); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142055, 63265, 2596, 'chrA07', 21988145, 'A', 'G', 866, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.26320); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142056, 63265, 2632, 'chrA07', 21988181, 'T', 'C', 878, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26730); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142057, 63265, 2737, 'chrA07', 21988286, 'G', 'A', 913, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26640); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142058, 63265, 2770, 'chrA07', 21988319, 'G', 'A', 924, 'Val', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.27220); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142059, 63265, 2800, 'chrA07', 21988349, 'C', 'T', 934, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142060, 63265, 2848, 'chrA07', 21988397, 'T', 'C', 950, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142061, 63265, 2878, 'chrA07', 21988427, 'T', 'C', 960, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142062, 63265, 2881, 'chrA07', 21988430, 'C', 'T', 961, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142063, 63265, 2890, 'chrA07', 21988439, 'G', 'A', 964, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142064, 63265, 2908, 'chrA07', 21988457, 'G', 'C', 970, 'Asp', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01320); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142065, 63265, 2941, 'chrA07', 21988490, 'A', 'T', 981, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.31170); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142066, 63265, 2968, 'chrA07', 21988517, 'C', 'T', 990, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.02880); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142067, 63265, 3163, 'chrA07', 21988712, 'G', 'A', 1055, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.27470); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142068, 63265, 3188, 'chrA07', 21988737, 'C', 'G', 1063, 'Ala', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.27550); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142069, 63265, 3199, 'chrA07', 21988748, 'A', 'T', 1067, 'Ser', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.32070); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142070, 63265, 3283, 'chrA07', 21988832, 'G', 'T', 1095, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142071, 63265, 3289, 'chrA07', 21988838, 'G', 'T', 1097, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327046, 1, 1319, 'chrC09', 9319194, 'G', 'A', 440, 'Ser', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327047, 1, 1085, 'chrC09', 9319428, 'C', 'T', 362, 'Arg', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327045, 2, 200, 'chrC09', 9311197, 'A', 'C', 67, 'His', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327036, 3, 385, 'chrC09', 9301658, 'T', 'A', 129, 'Phe', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327037, 3, 419, 'chrC09', 9301692, 'A', 'G', 140, 'Glu', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327038, 3, 726, 'chrC09', 9301999, 'C', 'G', 242, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327039, 3, 896, 'chrC09', 9302169, 'T', 'A', 299, 'Val', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00250); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327040, 3, 1106, 'chrC09', 9302379, 'G', 'T', 369, 'Arg', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00510); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327041, 3, 1220, 'chrC09', 9302493, 'A', 'T', 407, 'Glu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327042, 3, 1307, 'chrC09', 9302580, 'A', 'T', 436, 'His', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327043, 3, 1576, 'chrC09', 9302849, 'T', 'A', 526, 'Cys', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327044, 3, 1697, 'chrC09', 9302970, 'A', 'C', 566, 'Asn', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327035, 4, 67, 'chrC09', 9282013, 'C', 'A', 23, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327033, 5, 661, 'chrC09', 9273716, 'G', 'C', 221, 'Pro', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327034, 5, 481, 'chrC09', 9274017, 'A', 'T', 161, 'Leu', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327030, 6, 17, 'chrC09', 9267233, 'A', 'T', 6, 'Lys', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327031, 6, 305, 'chrC09', 9267521, 'G', 'C', 102, 'Gly', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327032, 6, 2093, 'chrC09', 9270136, 'G', 'T', 698, 'Gly', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327022, 7, 2450, 'chrC09', 9234630, 'G', 'T', 817, 'Ala', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00010); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327023, 7, 1718, 'chrC09', 9237814, 'A', 'C', 573, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00900); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327024, 7, 1408, 'chrC09', 9238193, 'T', 'C', 470, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327025, 7, 865, 'chrC09', 9238736, 'C', 'T', 289, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00200); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327026, 7, 825, 'chrC09', 9238776, 'G', 'T', 275, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.01230); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327027, 7, 763, 'chrC09', 9238838, 'A', 'G', 255, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327028, 7, 673, 'chrC09', 9238928, 'C', 'T', 225, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327029, 7, 612, 'chrC09', 9238989, 'A', 'T', 204, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327020, 8, 67, 'chrC09', 9230756, 'C', 'T', 23, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00350); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327021, 8, 81, 'chrC09', 9230770, 'G', 'C', 27, 'Glu', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.43170); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327018, 9, 169, 'chrC09', 9195157, 'T', 'C', 57, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00130); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327019, 9, 457, 'chrC09', 9195518, 'A', 'G', 153, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327014, 10, 191, 'chrC09', 9191243, 'G', 'A', 64, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.44000); -INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327015, 10, 188, 'chrC09', 9191246, 'G', 'T', 63, 'Pro', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); -INSERT INTO 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*/; + +USE `homologs_db`; + +-- +-- Table structure for table `homologs` +-- + +DROP TABLE IF EXISTS `homologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; CREATE TABLE `homologs` ( - `homologs_id` INT auto_increment, - `search_protein_name` varchar(45) NOT NULL, - `result_protein_name` varchar(45) NOT NULL, - `search_species_name` varchar(45) NOT NULL, - `result_species_name` varchar(45) NOT NULL, - `Percent_id` decimal(10, 5) NOT NULL, - `e_score` varchar(10) NOT NULL, - `is_search_structure` INT NOT NULL,/*1 represent has structure*/ - `is_result_structure` INT NOT NULL, - PRIMARY KEY (homologs_id) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; + `homologs_id` int NOT NULL AUTO_INCREMENT, + `search_protein_name` varchar(45) NOT NULL, + `result_protein_name` varchar(45) NOT NULL, + `search_species_name` varchar(45) NOT NULL, + `result_species_name` varchar(45) NOT NULL, + `Percent_id` decimal(10,5) NOT NULL, + `e_score` varchar(10) NOT NULL, + `is_search_structure` int NOT NULL, + `is_result_structure` int NOT NULL, + PRIMARY KEY (`homologs_id`) +) ENGINE=InnoDB AUTO_INCREMENT=1356306 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `homologs` +-- + +LOCK TABLES `homologs` WRITE; +/*!40000 ALTER TABLE `homologs` DISABLE KEYS */; +INSERT INTO `homologs` VALUES 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+/*!40000 ALTER TABLE `homologs` ENABLE KEYS */; +UNLOCK TABLES; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1, 'AT5G16970.1', 'BnaC09g40930D', 'arabidopsis', 'canola', 86.04700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (2, 'AT5G16970.1', 'BnaA10g17570D', 'arabidopsis', 'canola', 86.04700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (3, 'AT5G16970.1', 'BnaC03g08130D', 'arabidopsis', 'canola', 85.08800, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (4, 'AT5G16970.1', 'BnaA05g32330D', 'arabidopsis', 'canola', 81.63300, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (5, 'AT5G16970.1', 'BnaCnng06210D', 'arabidopsis', 'canola', 80.87000, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (6, 'AT5G16970.1', 'BnaA03g06330D', 'arabidopsis', 'canola', 85.37300, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (7, 'AT5G16970.1', 'BnaA09g28840D', 'arabidopsis', 'canola', 77.90700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (8, 'AT5G16970.1', 'BnaC05g20410D', 'arabidopsis', 'canola', 77.32600, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (9, 'AT5G16970.1', 'BnaC02g06960D', 'arabidopsis', 'canola', 76.23200, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (10, 'AT5G16970.1', 'BnaA02g03340D', 'arabidopsis', 'canola', 75.94200, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (11, 'AT4G32100.1', 'BnaC01g06360D', 'arabidopsis', 'canola', 55.28500, '2.18e-39'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (12, 'AT4G32100.1', 'BnaA01g04810D', 'arabidopsis', 'canola', 55.28500, '1.46e-38'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (13, 'AT4G32100.1', 'BnaA01g04820D', 'arabidopsis', 'canola', 52.84600, '6.47e-38'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (14, 'AT4G32100.1', 'BnaAnng05770D', 'arabidopsis', 'canola', 53.33300, '1.23e-37'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (15, 'AT4G32100.1', 'BnaC01g06960D', 'arabidopsis', 'canola', 51.61300, '1.19e-36'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (16, 'AT4G32100.1', 'BnaC07g18640D', 'arabidopsis', 'canola', 51.66700, '6.37e-36'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (17, 'AT4G32100.1', 'BnaA01g34870D', 'arabidopsis', 'canola', 49.19400, '4.15e-35'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (18, 'AT4G32100.1', 'BnaA02g24080D', 'arabidopsis', 'canola', 49.13800, '3.63e-27'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (19, 'AT4G32100.1', 'BnaA02g24090D', 'arabidopsis', 'canola', 48.27600, '6.69e-27'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (20, 'AT4G32100.1', 'BnaC02g31830D', 'arabidopsis', 'canola', 47.41400, '2.72e-25'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (21, 'AT2G43120.2', 'BnaC04g02730D', 'arabidopsis', 'canola', 90.96600, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (22, 'AT2G43120.2', 'BnaC03g24040D', 'arabidopsis', 'canola', 91.27700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (23, 'AT2G43120.2', 'BnaA03g20050D', 'arabidopsis', 'canola', 90.65400, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824264, 'BnaC07g23540D', 'AT5G65470.1', 'canola', 'arabidopsis', 39.72900, '9.91e-109'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824265, 'BnaC07g23540D', 'AT4G24530.1', 'canola', 'arabidopsis', 36.96500, '1.03e-108'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824266, 'BnaC07g23540D', 'AT2G01480.1', 'canola', 'arabidopsis', 41.78400, '2.97e-107'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824267, 'BnaC07g23540D', 'AT2G01480.2', 'canola', 'arabidopsis', 43.07700, '6.19e-104'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824268, 'BnaC07g23540D', 'AT1G14970.2', 'canola', 'arabidopsis', 40.00000, '1.03e-103'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824269, 'BnaC07g23540D', 'AT1G14970.1', 'canola', 'arabidopsis', 40.00000, '2.33e-102'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824270, 'BnaC07g23540D', 'AT1G14970.3', 'canola', 'arabidopsis', 40.24700, '2.02e-101'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824271, 'BnaC07g23540D', 'AT1G38065.2', 'canola', 'arabidopsis', 39.86200, '2.00e-95'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824272, 'BnaC07g23550D', 'AT3G26400.1', 'canola', 'arabidopsis', 77.19600, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824273, 'BnaC07g23550D', 'AT1G13020.1', 'canola', 'arabidopsis', 67.31400, '1.71e-180'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824274, 'BnaC07g23560D', 'AT3G26410.1', 'canola', 'arabidopsis', 93.21100, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824275, 'BnaC07g23570D', 'AT3G26420.1', 'canola', 'arabidopsis', 79.75700, '1.69e-126'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824276, 'BnaC07g23570D', 'AT2G21660.1', 'canola', 'arabidopsis', 60.49400, '1.99e-30'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824277, 'BnaC07g23570D', 'AT4G39260.3', 'canola', 'arabidopsis', 57.31700, '6.84e-30'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824278, 'BnaC07g23570D', 'AT5G04280.1', 'canola', 'arabidopsis', 41.95100, '2.88e-29'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824279, 'BnaC07g23570D', 'AT4G39260.2', 'canola', 'arabidopsis', 58.02500, '4.78e-29'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824280, 'BnaC07g23570D', 'AT1G60650.2', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824281, 'BnaC07g23570D', 'AT1G60650.1', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824282, 'BnaC07g23570D', 'AT4G39260.4', 'canola', 'arabidopsis', 56.06100, '2.46e-21'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824283, 'BnaC07g23580D', 'AT3G26430.1', 'canola', 'arabidopsis', 84.21100, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824284, 'BnaC07g23580D', 'AT1G67830.1', 'canola', 'arabidopsis', 60.58800, '2.97e-155'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824285, 'BnaC07g23580D', 'AT5G14450.1', 'canola', 'arabidopsis', 50.66000, '4.50e-131'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320148, 'BnaA10g09850D', 'BnaA10g09850D', 'canola', 'canola', 100.00000, '5.68e-110'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320149, 'BnaA10g09850D', 'BnaC09g32290D', 'canola', 'canola', 93.59000, '5.28e-93'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320150, 'BnaA10g09850D', 'BnaC02g12890D', 'canola', 'canola', 72.85700, '3.68e-26'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320151, 'BnaA10g09860D', 'BnaA10g09860D', 'canola', 'canola', 100.00000, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320152, 'BnaA10g09860D', 'BnaC09g32300D', 'canola', 'canola', 86.68300, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320153, 'BnaA10g09860D', 'BnaA02g08940D', 'canola', 'canola', 69.50900, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320154, 'BnaA10g09860D', 'BnaC02g12870D', 'canola', 'canola', 83.58500, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320155, 'BnaA10g09860D', 'BnaC08g12230D', 'canola', 'canola', 58.34400, '1.15e-177'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320156, 'BnaA10g09860D', 'BnaA01g15750D', 'canola', 'canola', 55.24900, '1.77e-162'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320157, 'BnaA10g09860D', 'BnaC01g18800D', 'canola', 'canola', 62.35600, '5.48e-116'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320158, 'BnaA10g09860D', 'BnaA06g19020D', 'canola', 'canola', 34.15200, '4.23e-50'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320159, 'BnaA10g09860D', 'BnaC09g05960D', 'canola', 'canola', 44.25500, '2.79e-46'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320160, 'BnaA10g09860D', 'BnaA06g22700D', 'canola', 'canola', 42.16900, '2.31e-43'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320161, 'BnaA10g09870D', 'BnaA10g09870D', 'canola', 'canola', 100.00000, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320162, 'BnaA10g09870D', 'BnaC09g32310D', 'canola', 'canola', 90.82800, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320163, 'BnaA10g09870D', 'BnaA02g08930D', 'canola', 'canola', 72.72700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320164, 'BnaA10g09870D', 'BnaC02g12860D', 'canola', 'canola', 70.51700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320165, 'BnaA10g09870D', 'BnaA03g11280D', 'canola', 'canola', 70.32600, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320166, 'BnaA10g09870D', 'BnaC03g71710D', 'canola', 'canola', 87.03700, '1.49e-113'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320167, 'BnaA10g09880D', 'BnaA10g09880D', 'canola', 'canola', 100.00000, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320168, 'BnaA10g09880D', 'BnaC09g32320D', 'canola', 'canola', 98.12600, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320169, 'BnaA10g09880D', 'BnaA02g08870D', 'canola', 'canola', 85.38300, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320170, 'BnaA10g09880D', 'BnaA01g20560D', 'canola', 'canola', 51.22000, '1.02e-130'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320171, 'BnaA10g09880D', 'BnaC01g25850D', 'canola', 'canola', 51.81100, '9.19e-130'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320172, 'BnaA10g09880D', 'BnaA06g19130D', 'canola', 'canola', 51.24000, '4.00e-128'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690828, 'BnaA07g31480D', 'AT1G74360.1', 'canola', 'arabidopsis', 84.02200, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690829, 'BnaA07g31480D', 'AT2G01950.1', 'canola', 'arabidopsis', 32.34200, '3.57e-149'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690830, 'BnaA07g31480D', 'AT1G55610.1', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690831, 'BnaA07g31480D', 'AT1G55610.2', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690832, 'BnaA07g31480D', 'AT1G17230.1', 'canola', 'arabidopsis', 32.44000, '7.99e-146'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690833, 'BnaA07g31480D', 'AT1G17230.2', 'canola', 'arabidopsis', 32.44000, '1.34e-145'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690834, 'BnaA07g31480D', 'AT4G39400.1', 'canola', 'arabidopsis', 33.15200, '5.71e-145'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690835, 'BnaA07g31480D', 'AT3G13380.1', 'canola', 'arabidopsis', 32.44600, '3.05e-143'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690836, 'BnaA07g31480D', 'AT5G63930.1', 'canola', 'arabidopsis', 33.05600, '1.84e-142'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690837, 'BnaA07g31480D', 'AT5G63930.2', 'canola', 'arabidopsis', 33.23900, '3.94e-141'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356296, 'BnaA07g31480D', 'BnaA07g31480D', 'canola', 'canola', 100.00000, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356297, 'BnaA07g31480D', 'BnaC06g35270D', 'canola', 'canola', 96.79400, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356298, 'BnaA07g31480D', 'BnaCnng50590D', 'canola', 'canola', 75.29100, '5.45e-180'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356299, 'BnaA07g31480D', 'BnaA02g11590D', 'canola', 'canola', 74.41900, '3.01e-178'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356300, 'BnaA07g31480D', 'BnaC05g13410D', 'canola', 'canola', 32.51300, '7.21e-153'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356301, 'BnaA07g31480D', 'BnaA06g11580D', 'canola', 'canola', 33.08800, '1.36e-152'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356302, 'BnaA07g31480D', 'BnaC07g47240D', 'canola', 'canola', 33.42600, '6.47e-151'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356303, 'BnaA07g31480D', 'BnaA01g05490D', 'canola', 'canola', 33.58100, '3.69e-148'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356304, 'BnaA07g31480D', 'BnaC07g21390D', 'canola', 'canola', 32.23900, '2.77e-147'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356305, 'BnaA07g31480D', 'BnaA06g34400D', 'canola', 'canola', 31.89600, '3.39e-147'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86750, 'AT1G74360.1', 'BnaC06g35270D', 'arabidopsis', 'canola', 84.27700, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86751, 'AT1G74360.1', 'BnaA07g31480D', 'arabidopsis', 'canola', 84.02200, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86752, 'AT1G74360.1', 'BnaA02g11590D', 'arabidopsis', 'canola', 77.97100, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86753, 'AT1G74360.1', 'BnaCnng50590D', 'arabidopsis', 'canola', 77.97100, '0.0'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86754, 'AT1G74360.1', 'BnaA08g00410D', 'arabidopsis', 'canola', 31.84900, '5.39e-154'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86755, 'AT1G74360.1', 'BnaA06g11580D', 'arabidopsis', 'canola', 33.86600, '3.20e-153'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86756, 'AT1G74360.1', 'BnaA02g16780D', 'arabidopsis', 'canola', 67.03000, '2.11e-152'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86757, 'AT1G74360.1', 'BnaA06g34400D', 'arabidopsis', 'canola', 32.93200, '1.50e-151'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86758, 'AT1G74360.1', 'BnaA08g16520D', 'arabidopsis', 'canola', 33.89500, '1.68e-150'); -INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86759, 'AT1G74360.1', 'BnaC07g47240D', 'arabidopsis', 'canola', 33.88700, '3.05e-150'); +-- Dump completed on 2025-03-29 19:28:31 diff --git a/config/init.sh b/config/init.sh index 50b7f102..68aff95b 100755 --- a/config/init.sh +++ b/config/init.sh @@ -14,6 +14,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/embryo.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant2.sql @@ -23,6 +24,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/llama3.sql @@ -40,9 +42,6 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/striga.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql - echo "Data are now loaded. Preparing API config" echo "Please manually edit config file!" diff --git a/requirements.txt b/requirements.txt index 26578917..56cc25dc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,31 +1,31 @@ aniso8601==10.0.0 async-timeout==5.0.1 -attrs==25.1.0 +attrs==25.3.0 black==25.1.0 blinker==1.9.0 cachelib==0.9.0 certifi==2025.1.31 charset-normalizer==3.4.1 click==8.1.8 -coverage==7.6.10 +coverage==7.7.1 Deprecated==1.2.18 -flake8==7.1.1 +flake8==7.2.0 Flask==3.1.0 -Flask-Caching==2.3.0 -Flask-Cors==5.0.0 -Flask-Limiter==3.10.1 +Flask-Caching==2.3.1 +flask-cors==5.0.1 +Flask-Limiter==3.12 flask-marshmallow==1.3.0 flask-restx==1.3.0 Flask-SQLAlchemy==3.1.1 greenlet==3.1.1 idna==3.10 importlib_resources==6.5.2 -iniconfig==2.0.0 +iniconfig==2.1.0 itsdangerous==2.2.0 -Jinja2==3.1.5 +Jinja2==3.1.6 jsonschema==4.23.0 jsonschema-specifications==2024.10.1 -limits==4.0.1 +limits==4.4.1 markdown-it-py==3.0.0 MarkupSafe==3.0.2 marshmallow==3.26.1 @@ -36,24 +36,24 @@ mysqlclient==2.2.7 ordered-set==4.1.0 packaging==24.2 pathspec==0.12.1 -platformdirs==4.3.6 +platformdirs==4.3.7 pluggy==1.5.0 -pycodestyle==2.12.1 -pyflakes==3.2.0 +pycodestyle==2.13.0 +pyflakes==3.3.0 Pygments==2.19.1 pyrsistent==0.20.0 -pytest==8.3.4 +pytest==8.3.5 python-dateutil==2.9.0.post0 -pytz==2025.1 +pytz==2025.2 redis==5.2.1 referencing==0.36.2 requests==2.32.3 rich==13.9.4 -rpds-py==0.22.3 -setuptools==75.8.0 +rpds-py==0.24.0 +setuptools==78.1.0 six==1.17.0 -SQLAlchemy==2.0.38 -typing_extensions==4.12.2 +SQLAlchemy==2.0.40 +typing_extensions==4.13.0 urllib3==2.3.0 Werkzeug==3.1.3 wheel==0.45.1 diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index c53156ca..b634a88d 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -115,9 +115,9 @@ def test_get_snps(self): "protein_coding", "CODING", "GSBRNA2T00000007001", - 0.0066 + 0.0066, ] - ] + ], } self.assertEqual(response.json, expected) From c23fddc1cdf9219dae08c259b73b2c0e91276740 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 29 Mar 2025 19:44:46 -0400 Subject: [PATCH 12/14] Deprecated Python 3.9 --- .github/workflows/bar-api.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index d858b375..97890ad5 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - python-version: [3.9, 3.10.15, 3.11, 3.12, 3.13] + python-version: [3.10.16, 3.11, 3.12, 3.13] services: redis: From 6931de17512b9ad280903328056ec2532e0e2cbf Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 19 Apr 2025 17:04:53 -0400 Subject: [PATCH 13/14] Updated dependancies. --- .github/workflows/bar-api.yml | 2 +- Dockerfile | 2 +- docker-compose.yml | 4 +-- docs/requirements.txt | 48 +++++++++++++++++++---------------- requirements.txt | 18 ++++++------- 5 files changed, 39 insertions(+), 35 deletions(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index 97890ad5..3ab318e4 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - python-version: [3.10.16, 3.11, 3.12, 3.13] + python-version: [3.10.17, 3.11, 3.12, 3.13] services: redis: diff --git a/Dockerfile b/Dockerfile index 5aea5065..48efcf7b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-bookworm +FROM python:3.13-bookworm WORKDIR /usr/src/app diff --git a/docker-compose.yml b/docker-compose.yml index 2e690b54..5559c369 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,14 +1,14 @@ services: mysqldb: - image: mysql:9.0.1 + image: mysql:9.3.0 container_name: BAR_mysqldb restart: always environment: - MYSQL_ROOT_PASSWORD=root redis: - image: redis:7.2.5 + image: redis:7.4.2 container_name: BAR_redis restart: always ports: diff --git a/docs/requirements.txt b/docs/requirements.txt index 5bcfd2fa..f73d28e2 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,27 +1,31 @@ -alabaster==0.7.16 -Babel==2.14.0 -beautifulsoup4==4.12.3 -certifi==2024.2.2 -charset-normalizer==3.3.2 +alabaster==1.0.0 +babel==2.17.0 +beautifulsoup4==4.13.4 +certifi==2025.1.31 +charset-normalizer==3.4.1 docutils==0.21.2 -furo==2024.4.27 -idna==3.7 +furo==2024.8.6 +idna==3.10 imagesize==1.4.1 -Jinja2==3.1.3 -MarkupSafe==2.1.5 -packaging==24.0 -Pygments==2.17.2 -pytz==2024.1 -requests==2.31.0 +Jinja2==3.1.6 +MarkupSafe==3.0.2 +packaging==25.0 +Pygments==2.19.1 +pytz==2025.2 +requests==2.32.3 +roman-numerals-py==3.1.0 +setuptools==78.1.1 snowballstemmer==2.2.0 -soupsieve==2.5 -Sphinx==7.3.7 -sphinx-basic-ng==1.0.0b1 +soupsieve==2.6 +Sphinx==8.2.3 +sphinx-basic-ng==1.0.0b2 sphinx-copybutton==0.5.2 -sphinxcontrib-applehelp==1.0.8 -sphinxcontrib-devhelp==1.0.6 -sphinxcontrib-htmlhelp==2.0.5 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.7 -sphinxcontrib-serializinghtml==1.1.10 -urllib3==2.2.1 +sphinxcontrib-qthelp==2.0.0 +sphinxcontrib-serializinghtml==2.0.0 +typing_extensions==4.13.2 +urllib3==2.4.0 +wheel==0.45.1 diff --git a/requirements.txt b/requirements.txt index 56cc25dc..41ef7a8a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -aniso8601==10.0.0 +aniso8601==10.0.1 async-timeout==5.0.1 attrs==25.3.0 black==25.1.0 @@ -7,7 +7,7 @@ cachelib==0.9.0 certifi==2025.1.31 charset-normalizer==3.4.1 click==8.1.8 -coverage==7.7.1 +coverage==7.8.0 Deprecated==1.2.18 flake8==7.2.0 Flask==3.1.0 @@ -17,7 +17,7 @@ Flask-Limiter==3.12 flask-marshmallow==1.3.0 flask-restx==1.3.0 Flask-SQLAlchemy==3.1.1 -greenlet==3.1.1 +greenlet==3.2.0 idna==3.10 importlib_resources==6.5.2 iniconfig==2.1.0 @@ -25,10 +25,10 @@ itsdangerous==2.2.0 Jinja2==3.1.6 jsonschema==4.23.0 jsonschema-specifications==2024.10.1 -limits==4.4.1 +limits==5.0.0 markdown-it-py==3.0.0 MarkupSafe==3.0.2 -marshmallow==3.26.1 +marshmallow==4.0.0 mccabe==0.7.0 mdurl==0.1.2 mypy-extensions==1.0.0 @@ -39,7 +39,7 @@ pathspec==0.12.1 platformdirs==4.3.7 pluggy==1.5.0 pycodestyle==2.13.0 -pyflakes==3.3.0 +pyflakes==3.3.2 Pygments==2.19.1 pyrsistent==0.20.0 pytest==8.3.5 @@ -50,11 +50,11 @@ referencing==0.36.2 requests==2.32.3 rich==13.9.4 rpds-py==0.24.0 -setuptools==78.1.0 +setuptools==78.1.1 six==1.17.0 SQLAlchemy==2.0.40 -typing_extensions==4.13.0 -urllib3==2.3.0 +typing_extensions==4.13.2 +urllib3==2.4.0 Werkzeug==3.1.3 wheel==0.45.1 wrapt==1.17.2 From 808e40675aae2063b4507ba68ae9c3044b377a0c Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 19 Apr 2025 17:23:33 -0400 Subject: [PATCH 14/14] Minor fix. --- tests/resources/test_proxy.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/resources/test_proxy.py b/tests/resources/test_proxy.py index f7467b8e..aca80e58 100644 --- a/tests/resources/test_proxy.py +++ b/tests/resources/test_proxy.py @@ -25,7 +25,6 @@ def test_get_atted_api5(self): # If no data, the service should return this response response = self.app_client.get("/proxy/atted_api5/At1g01011/5") - expected = {"error": "No gene ID specified.", "status_code": 400} self.assertEqual(response.json, expected)