5e03648c60553bf87f9399b4dd070e5ef79a8074 gperez2 Tue Jul 1 12:38:28 2025 -0700 Code review edits, refs #36009 diff --git src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra index 1a6ee3849aa..7502187a412 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra @@ -1,248 +1,248 @@ track wgEncodeGencodeV48 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel All GENCODE V48 longLabel All GENCODE annotations from V48 (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 48 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 wgEncodeGencodeV48ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeV48 type genePred idXref wgEncodeGencodeAttrsV48 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsV48 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 wgEncodeGencodeAttrsV48 order by transcriptType' hg38 # - 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 wgEncodeGencodeTagV48 order by tag' hg38 # - 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=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,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,rRNA_pseudogene,scaRNA,snoRNA,snRNA,sRNA,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_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,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=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,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,rRNA_pseudogene,scaRNA,snoRNA,snRNA,sRNA,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_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,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 wgEncodeGencodeBasicV48 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version 48 (Ensembl 114) type genePred priority 1 track wgEncodeGencodeCompV48 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version 48 (Ensembl 114) type genePred priority 2 track wgEncodeGencodePseudoGeneV48 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version 48 (Ensembl 114) type genePred color 255,51,255 priority 3 track wgEncodeGencodeV48ViewPolya shortLabel PolyA view cPolya visibility hide subTrack wgEncodeGencodeV48 type genePred configurable off track wgEncodeGencodePolyaV48 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV48ViewPolya off subGroups view=bPolya name=zPolyA shortLabel PolyA longLabel PolyA Transcript Annotation Set from GENCODE Version 48 (Ensembl 114) type genePred color 0,0,0 priority 5 # searches for basic searchName wgEncodeGencodeBasicV48 searchTable wgEncodeGencodeBasicV48 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24901 searchName wgEncodeGencodeBasicGeneSymV48 searchTable wgEncodeGencodeBasicV48 searchMethod exact searchType genePred searchPriority 2.24902 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneV48 searchTable wgEncodeGencodeBasicV48 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24903 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptV48 searchTable wgEncodeGencodeBasicV48 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24904 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneV48 searchTable wgEncodeGencodeBasicV48 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24906 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeBasicProtV48 searchTable wgEncodeGencodeBasicV48 searchMethod prefix searchType genePred termRegex ENSP[0-9.]+ searchPriority 2.24907 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for comp searchName wgEncodeGencodeCompV48 searchTable wgEncodeGencodeCompV48 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24908 searchName wgEncodeGencodeCompGeneSymV48 searchTable wgEncodeGencodeCompV48 searchMethod exact searchType genePred searchPriority 2.24909 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneV48 searchTable wgEncodeGencodeCompV48 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24910 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptV48 searchTable wgEncodeGencodeCompV48 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24911 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneV48 searchTable wgEncodeGencodeCompV48 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24912 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeCompProtV48 searchTable wgEncodeGencodeCompV48 searchMethod prefix searchType genePred termRegex ENSP[0-9.]+ searchPriority 2.24913 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneV48 searchTable wgEncodeGencodePseudoGeneV48 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24914 searchName wgEncodeGencodePseudoGeneGeneSymV48 searchTable wgEncodeGencodePseudoGeneV48 searchMethod exact searchType genePred searchPriority 2.24915 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneV48 searchTable wgEncodeGencodePseudoGeneV48 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24916 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptV48 searchTable wgEncodeGencodePseudoGeneV48 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24917 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneV48 searchTable wgEncodeGencodePseudoGeneV48 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24918 xrefTable wgEncodeGencodeAttrsV48 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'