From b597e2bcd5fced0e59813a30f548160c5fe4fbb9 Mon Sep 17 00:00:00 2001 From: JackieMium Date: Fri, 20 Feb 2026 17:43:33 -0600 Subject: [PATCH 1/2] add --skip-ssl option to mysql queries --- R/trackplot.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/trackplot.R b/R/trackplot.R index bc30308..1a64d00 100644 --- a/R/trackplot.R +++ b/R/trackplot.R @@ -1821,7 +1821,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = } cmd = paste0( - "mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", + "mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name, gieStain from ", tblName, " WHERE chrom =\"", chr, @@ -1897,7 +1897,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = .check_mysql() - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name from ", tbl, " WHERE chrom =\"", tar_chr, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name from ", tbl, " WHERE chrom =\"", tar_chr, "\"'") message(paste0("Extracting chromHMM from UCSC:\n", " chromosome: ", tar_chr, "\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd) @@ -1921,7 +1921,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = .check_mysql() op_file = tempfile(pattern = "ucsc", fileext = ".tsv") - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE name2 =\"", genesymbol, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE name2 =\"", genesymbol, "\"'") message(paste0("Extracting gene models from UCSC:\n", " Gene: ", genesymbol, "\n", " build: ", refBuild, "\n query: ", cmd)) ucsc = data.table::fread(cmd = cmd, sep = "\t") @@ -1946,7 +1946,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = tar_chr = chr } - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE chrom =\"", tar_chr, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE chrom =\"", tar_chr, "\"'") message(paste0("Extracting gene models from UCSC:\n", " chromosome: ", tar_chr, "\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd) @@ -2159,7 +2159,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = temp_op_bed = tempfile(pattern = "profileplot_ucsc", tmpdir = op_dir, fileext = ".bed") - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2 from refGene'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2 from refGene'") message(paste0("Extracting gene models from UCSC:\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd) From a4982c24f339f24c63e2688c163fe62b1ee5fea3 Mon Sep 17 00:00:00 2001 From: JackieMium Date: Sat, 28 Feb 2026 16:42:49 -0600 Subject: [PATCH 2/2] Add default verbose=FALSE option --- R/trackplot.R | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/R/trackplot.R b/R/trackplot.R index 1a64d00..25fd12f 100644 --- a/R/trackplot.R +++ b/R/trackplot.R @@ -1701,7 +1701,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = lo_h_ord[lord] } -.gen_windows = function(chr = NA, start, end, window_size = 50, op_dir = getwd()){ +.gen_windows = function(chr = NA, start, end, window_size = 50, op_dir = getwd(), verbose = FALSE){ #chr = "chr19"; start = 15348301; end = 15391262; window_size = 50; op_dir = getwd() message(paste0("Generating windows ", "[", window_size, " bp window size]")) @@ -1714,7 +1714,9 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = window_dat$chr = chr window_dat = window_dat[, .(chr, start, end)] - print(window_dat) + if(verbose) { + print(window_dat) + } op_dir = paste0(op_dir, "/") @@ -1813,7 +1815,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = } } -.extract_cytoband = function(chr = NULL, refBuild = "hg19", tblName = "cytoBand"){ +.extract_cytoband = function(chr = NULL, refBuild = "hg19", tblName = "cytoBand", verbose = FALSE){ if(!grepl(pattern = "^chr", x = chr)){ message("Adding chr prefix to target chromosome for UCSC query..") @@ -1827,8 +1829,9 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = chr, "\"'" ) - message(paste0("Extracting cytobands from UCSC:\n", " chromosome: ", chr, "\n", " build: ", refBuild, "\n query: ", cmd)) - + if(verbose){ + message(paste0("Extracting cytobands from UCSC:\n", " chromosome: ", chr, "\n", " build: ", refBuild, "\n query: ", cmd)) + } cyto = data.table::fread(cmd = cmd, colClasses = c("character", "numeric", "numeric", "character", "character")) colnames(cyto) = c("chr", "start", "end", "band", "stain") data.table::setkey(x = cyto, chr, start, end) @@ -2035,7 +2038,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = } .collapse_tx = function(exon_tbls){ - message("Collapsing transcripts..") + #message("Collapsing transcripts..") tx_tbl = lapply(exon_tbls, function(x){ xdt = data.table::data.table(start = x[[1]], end = x[[2]]) xdt$tx = attr(x = x, which = "tx")