From c2f2cafb28a83f57d0f2530a287da3c08b7fe8cb Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Fri, 20 Mar 2026 12:24:44 -0400 Subject: [PATCH 1/9] First pass at antismash query --- .../lib/wdk/model/questions/geneQuestions.xml | 29 ++++++++ .../wdk/model/questions/params/geneParams.xml | 74 +++++++++++++++++++ .../model/questions/params/organismParams.xml | 40 ++++++++++ .../model/questions/queries/geneQueries.xml | 45 +++++++++++ 4 files changed, 188 insertions(+) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 7690d0569..907692a2e 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -931,6 +931,35 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index fa686ea6a..6bbb98eba 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5104,6 +5104,29 @@ products of your selected type (or types).

+ + + Select one or more secondary metabolite cluster categories. + + + + + Select an annotation. Options filter based on the selected category. + + + @@ -9711,6 +9734,57 @@ end as term + + + + + + + + + + + + + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 5fb56512b..f89f7de75 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -438,6 +438,21 @@ + + Select the organism(s) to search. + + pruneNodesWithSingleExtendingChild + showOnlyPreferredOrganisms + + + @@ -1170,6 +1185,31 @@ + + + + + + + + + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index c0163792a..51f742bf8 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5769,6 +5769,51 @@ select distinct ta.gene_source_id + + + + + + + + + + + + + + + + + + + From 2044a0b30bbaa3f54d2c39122d50002a2032ef83 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Fri, 20 Mar 2026 13:49:55 -0400 Subject: [PATCH 2/9] Add attributes and summary --- Model/lib/wdk/model/questions/geneQuestions.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 907692a2e..2a7a1a95d 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,9 +948,17 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + + + Date: Fri, 20 Mar 2026 13:50:41 -0400 Subject: [PATCH 3/9] Add default and fix depended params --- Model/lib/wdk/model/questions/params/geneParams.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 6bbb98eba..53c194780 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5113,7 +5113,7 @@ products of your selected type (or types).

dependedParamRef="organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select one or more secondary metabolite cluster categories. - +
prompt="Annotation" multiPick="true" quote="true" - dependedParamRef="geneParams.antismash_category" + dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select an annotation. Options filter based on the selected category. From ca1c9fef4530f546ea041e9b04a0116cac3a2d7c Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:55:17 -0400 Subject: [PATCH 4/9] Add quotes to project_id macro --- Model/lib/wdk/model/questions/params/organismParams.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index f89f7de75..d3dae0663 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -1196,7 +1196,7 @@ FROM apidbtuning.geneattributes ga , apidb.antismashfeature af WHERE ga.na_feature_id = af.na_feature_id - AND (ga.project_id = @PROJECT_ID@ OR 'UniDB' = @PROJECT_ID@) + AND (ga.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@') ) SELECT DISTINCT term , parentTerm From fce6d016a8d9b1d6faa112e3ec7dc9038748f39e Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:56:29 -0400 Subject: [PATCH 5/9] Defaults and ordering --- .../lib/wdk/model/questions/params/geneParams.xml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 53c194780..6d05bb687 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -5113,7 +5113,7 @@ products of your selected type (or types).

dependedParamRef="organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select one or more secondary metabolite cluster categories. - +
dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism" includeProjects="FungiDB,UniDB"> Select an annotation. Options filter based on the selected category. - + @@ -9767,6 +9769,11 @@ end as term From 1dced116f0851066d2feedd41ee5bf3ccbd76ef6 Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 11:57:18 -0400 Subject: [PATCH 6/9] Multipick, so no option for any --- Model/lib/wdk/model/questions/queries/geneQueries.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 51f742bf8..2cd87f618 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5808,7 +5808,6 @@ select distinct ta.gene_source_id AND (af.antismash_annotation IN ($$antismash_annotation$$) -- OR ($$antismash_annotation$$ = 'biosynthetic any' AND af.antismash_annotation like 'biosynthetic%') OR ($$antismash_annotation$$ = 'unknown' AND af.antismash_annotation IS NULL) - OR ($$antismash_annotation$$ = 'any') ) ]]> From c91c9a2ea59834928f5c2123a8c91f671f41473a Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 13:09:09 -0400 Subject: [PATCH 7/9] Fix to handle genes that appear in more than one cluster --- .../model/questions/queries/geneQueries.xml | 66 ++++++++++++------- 1 file changed, 43 insertions(+), 23 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 2cd87f618..c7312a10e 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5783,32 +5783,52 @@ select distinct ta.gene_source_id + From 557375c3dd456eb9c2460a410c286ef0d50a9c1b Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Tue, 24 Mar 2026 13:09:39 -0400 Subject: [PATCH 8/9] Add overlapping clusters column --- Model/lib/wdk/model/questions/geneQuestions.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 2a7a1a95d..b2b83232f 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,7 +948,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " @@ -957,6 +957,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + From b6eae0fa810e0a23da7f62372802fc618353aedb Mon Sep 17 00:00:00 2001 From: Kathryn Crouch Date: Thu, 26 Mar 2026 11:00:41 -0400 Subject: [PATCH 9/9] Add JBrowse links in results --- .../lib/wdk/model/questions/geneQuestions.xml | 12 ++++- .../model/questions/queries/geneQueries.xml | 49 ++++++++++++------- 2 files changed, 43 insertions(+), 18 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index b2b83232f..d9b5e1ac1 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -948,7 +948,7 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " @@ -957,7 +957,17 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as " + + + + + + $$sequence_id$$:$$cluster_start$$-$$cluster_end$$ + ]]> + + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index c7312a10e..6202067fe 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5783,12 +5783,16 @@ select distinct ta.gene_source_id + + + ', + gc2.sequence_id, ':', gc2.cluster_start, '-', gc2.cluster_end, '' + ), + ', ' ORDER BY gc2.cluster_start + ) AS overlapping_clusters + FROM ranked r + JOIN gene_clusters gc2 + ON gc2.source_id = r.source_id + AND gc2.antismash_cluster_id != r.antismash_cluster_id + WHERE r.rn = 1 + GROUP BY r.source_id ) - SELECT source_id, gene_source_id, project_id, + SELECT r.source_id, r.gene_source_id, r.project_id, 10 AS wdk_weight, 'Y' AS matched_result, - category, antismash_annotation, cluster_start, cluster_end, sequence_id, - overlapping_clusters - FROM ranked - WHERE rn = 1 + r.category, r.antismash_annotation, r.cluster_start, r.cluster_end, r.sequence_id, + r.org_abbrev, + GREATEST(r.cluster_start - 1000, 1) AS cluster_context_start, + r.cluster_end + 1000 AS cluster_context_end, + COALESCE(go.overlapping_clusters, 'No') AS overlapping_clusters + FROM ranked r + LEFT JOIN gene_overlaps go ON go.source_id = r.source_id + WHERE r.rn = 1 ]]>