5e03648c60553bf87f9399b4dd070e5ef79a8074 gperez2 Tue Jul 1 12:38:28 2025 -0700 Code review edits, refs #36009 diff --git src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra index 402a4019ac1..5ed4cf41663 100644 --- src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra +++ src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra @@ -1,248 +1,248 @@ track wgEncodeGencodeVM37 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel All GENCODE VM37 longLabel All GENCODE annotations from VM37 (Ensembl 114) group genes dragAndDrop subTracks priority 2.947 visibility pack subGroup1 view View aGenes=Genes bPolya=PolyA subGroup2 name Name Basic=Basic Comprehensive=Comprehensive Pseudogenes=Pseudogenes zPolyA=PolyA allButtonPair on sortOrder name=+ view=+ fileSortOrder labVersion=Contents dccAccession=UCSC_Accession type genePred configurable off wgEncodeGencodeVersion M37 maxTransEnabled on -pennantIcon New red ../goldenPath/newsarch.html#062425 "Updated June 24, 2025" +pennantIcon New red ../goldenPath/newsarch.html#062425 "New June 24, 2025" track wgEncodeGencodeVM37ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeVM37 type genePred idXref wgEncodeGencodeAttrsVM37 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsVM37 itemClassNameColumn transcriptId itemClassClassColumn transcriptClass cdsDrawDefault genomic\ codons baseColorUseCds given baseColorDefault genomicCodons geneClasses coding nonCoding pseudo problem gClass_coding 12,12,120 gClass_nonCoding 0,153,0 gClass_pseudo 255,51,255 gClass_problem 254,0,0 highlightColor 255,255,0 # filterBy notes: # - attrs is an alias for the current wgEncodeGencodeAttrs in the sql # - transcriptMethod is a pseudo-column name, which is handled explictly in the code # - attrs.transcriptType are transcript biotypes. This will get the current list of values: # hgsql -Ne 'select distinct(transcriptType) from wgEncodeGencodeAttrsVM37 order by transcriptType' mm39 # - tag - is s pseudo-column name for join with the tag table. This will get the current list of values: # hgsql -Ne 'select distinct(tag) from wgEncodeGencodeTagVM37 order by tag' mm39 # - supportLevel is a pseudo-column name handled in the code filterBy attrs.transcriptClass:Transcript_Class=coding,nonCoding,pseudo,problem \ transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only \ attrs.transcriptType:Transcript_Biotype=IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_D_pseudogene,IG_J_gene,IG_LV_gene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF \ supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA highlightBy transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only \ attrs.transcriptType:Transcript_Biotype=IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_D_pseudogene,IG_J_gene,IG_LV_gene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF \ supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA track wgEncodeGencodeBasicVM37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM37ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version M37 (Ensembl 114) type genePred priority 1 track wgEncodeGencodeCompVM37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM37ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version M37 (Ensembl 114) type genePred priority 2 track wgEncodeGencodePseudoGeneVM37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM37ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version M37 (Ensembl 114) type genePred color 255,51,255 priority 3 track wgEncodeGencodeVM37ViewPolya shortLabel PolyA view cPolya visibility hide subTrack wgEncodeGencodeVM37 type genePred configurable off track wgEncodeGencodePolyaVM37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM37ViewPolya off subGroups view=bPolya name=zPolyA shortLabel PolyA longLabel PolyA Transcript Annotation Set from GENCODE Version M37 (Ensembl 114) type genePred color 0,0,0 priority 5 # searches for basic searchName wgEncodeGencodeBasicVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23701 searchName wgEncodeGencodeBasicGeneSymVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod exact searchType genePred searchPriority 2.23702 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23703 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23704 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23706 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeBasicProtVM37 searchTable wgEncodeGencodeBasicVM37 searchMethod prefix searchType genePred termRegex ENSMUSP[0-9.]+ searchPriority 2.23707 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for comp searchName wgEncodeGencodeCompVM37 searchTable wgEncodeGencodeCompVM37 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23708 searchName wgEncodeGencodeCompGeneSymVM37 searchTable wgEncodeGencodeCompVM37 searchMethod exact searchType genePred searchPriority 2.23709 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneVM37 searchTable wgEncodeGencodeCompVM37 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23710 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptVM37 searchTable wgEncodeGencodeCompVM37 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23711 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneVM37 searchTable wgEncodeGencodeCompVM37 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23712 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeCompProtVM37 searchTable wgEncodeGencodeCompVM37 searchMethod prefix searchType genePred termRegex ENSMUSP[0-9.]+ searchPriority 2.23713 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneVM37 searchTable wgEncodeGencodePseudoGeneVM37 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23714 searchName wgEncodeGencodePseudoGeneGeneSymVM37 searchTable wgEncodeGencodePseudoGeneVM37 searchMethod exact searchType genePred searchPriority 2.23715 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneVM37 searchTable wgEncodeGencodePseudoGeneVM37 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23716 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptVM37 searchTable wgEncodeGencodePseudoGeneVM37 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23717 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneVM37 searchTable wgEncodeGencodePseudoGeneVM37 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23718 xrefTable wgEncodeGencodeAttrsVM37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'