5e03648c60553bf87f9399b4dd070e5ef79a8074 gperez2 Tue Jul 1 12:38:28 2025 -0700 Code review edits, refs #36009 diff --git src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra index ad06a108f4b..aa7857c8032 100644 --- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra +++ src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra @@ -1,211 +1,211 @@ track wgEncodeGencodeV48lift37 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel GENCODE V48lift37 longLabel GENCODE lifted annotations from V48lift37 (Ensembl 114) group genes dragAndDrop subTracks priority 34.157 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 48lift37 -pennantIcon New red ../goldenPath/newsarch.html#062425 "Updated June 24, 2025" +pennantIcon New red ../goldenPath/newsarch.html#062425 "New June 24, 2025" track wgEncodeGencodeV48lift37ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeV48lift37 type genePred idXref wgEncodeGencodeAttrsV48lift37 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsV48lift37 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 wgEncodeGencodeAttrsV48lift37 order by transcriptType' hg19 # - 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 wgEncodeGencodeTagV48lift37 order by tag' hg19 # - 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=antisense,artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,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,rRNA_pseudogene,sense_intronic,sense_overlapping,snoRNA,snRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_candidate,appris_candidate_longest,appris_principal,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,artifactual_duplication,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,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,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,PAR,polymorphic_pseudogene_no_stop,precursor_RNA,pseudo_consens,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=antisense,artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,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,rRNA_pseudogene,sense_intronic,sense_overlapping,snoRNA,snRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_candidate,appris_candidate_longest,appris_principal,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,artifactual_duplication,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,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,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,PAR,polymorphic_pseudogene_no_stop,precursor_RNA,pseudo_consens,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 wgEncodeGencodeBasicV48lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48lift37ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version 48lift37 (Ensembl 114) type genePred priority 1 track wgEncodeGencodeCompV48lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48lift37ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version 48lift37 (Ensembl 114) type genePred priority 2 track wgEncodeGencodePseudoGeneV48lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48lift37ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version 48lift37 (Ensembl 114) type genePred color 255,51,255 priority 3 # searches for basic searchName wgEncodeGencodeBasicV48lift37 searchTable wgEncodeGencodeBasicV48lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24901 searchName wgEncodeGencodeBasicGeneSymV48lift37 searchTable wgEncodeGencodeBasicV48lift37 searchMethod exact searchType genePred searchPriority 2.24902 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneV48lift37 searchTable wgEncodeGencodeBasicV48lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24903 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptV48lift37 searchTable wgEncodeGencodeBasicV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24904 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneV48lift37 searchTable wgEncodeGencodeBasicV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24906 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' # searches for comp searchName wgEncodeGencodeCompV48lift37 searchTable wgEncodeGencodeCompV48lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24908 searchName wgEncodeGencodeCompGeneSymV48lift37 searchTable wgEncodeGencodeCompV48lift37 searchMethod exact searchType genePred searchPriority 2.24909 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneV48lift37 searchTable wgEncodeGencodeCompV48lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24910 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptV48lift37 searchTable wgEncodeGencodeCompV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24911 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneV48lift37 searchTable wgEncodeGencodeCompV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24912 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneV48lift37 searchTable wgEncodeGencodePseudoGeneV48lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24914 searchName wgEncodeGencodePseudoGeneGeneSymV48lift37 searchTable wgEncodeGencodePseudoGeneV48lift37 searchMethod exact searchType genePred searchPriority 2.24915 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneV48lift37 searchTable wgEncodeGencodePseudoGeneV48lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24916 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptV48lift37 searchTable wgEncodeGencodePseudoGeneV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24917 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneV48lift37 searchTable wgEncodeGencodePseudoGeneV48lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24918 xrefTable wgEncodeGencodeAttrsV48lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'