cfda5d697701c33ce782310b6343ad3469791620 lrnassar Wed Jul 17 17:08:36 2024 -0700 Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008 diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index 26d25db..6ef84a9 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,195 +1,194 @@ track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq genes from NCBI group genes visibility dense type genePred dragAndDrop subTracks noInherit on #subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq allButtonPair on dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt priority 2 dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="http://www.informatics.jax.org/marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$" dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase" track ncbiRefSeq parent refSeqComposite on color 12,12,120 shortLabel RefSeq All longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite off shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite off shortLabel RefSeq Other longLabel NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb type bigBed 12 + labelFields gene skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" track ncbiRefSeqPsl priority 5 parent refSeqComposite off shortLabel RefSeq Alignments longLabel RefSeq Alignments of RNAs type psl indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffCodons pslSequence no baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq baseColorUseCds table ncbiRefSeqCds idXref ncbiRefSeqLink mrnaAcc name color 0,0,0 pepTable ncbiRefSeqPepTable track ncbiRefSeqGenomicDiff parent refSeqComposite off priority 6 type bigBed 9 + skipEmptyFields on shortLabel RefSeq Diffs longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb itemRgb on track refGene override parent refSeqComposite off shortLabel UCSC RefSeq longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*) color 12,12,120 type genePred refPep refMrna idXref hgFixed.refLink mrnaAcc name - dataVersion priority 7 baseColorUseCds given baseColorDefault genomicCodons track ncbiRefSeqHgmd parent refSeqComposite off priority 9 type genePred shortLabel RefSeq HGMD longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons searchName ncbiRefSeqCuratedName2 searchTable ncbiRefSeqCurated searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07200 searchName ncbiRefSeqPredictedName2 searchTable ncbiRefSeqPredicted searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07201 searchName ncbiRefSeqCuratedProtAcc searchTable ncbiRefSeqCurated searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex [NY]P_[0-9]+(\.[0-9]+)? dontCheck XP_[0-9]+(\.[0-9]+)? searchPriority 2.07201 searchName ncbiRefSeqPredictedProtAcc searchTable ncbiRefSeqPredicted searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex XP_[0-9]+(\.[0-9]+)? dontCheck [NY]P_[0-9]+(\.[0-9]+)? searchPriority 2.07203 searchName ncbiRefSeqCuratedProduct searchTable ncbiRefSeqCurated searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07201 searchName ncbiRefSeqPredictedProduct searchTable ncbiRefSeqPredicted searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07203 searchTable ncbiRefSeqCurated searchMethod exact searchType genePred semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchName ncbiRefSeqCuratedNoVersion searchTable ncbiRefSeqCurated query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]* dontCheck [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchTable ncbiRefSeqPredicted searchMethod exact searchType genePred semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchName ncbiRefSeqPredictedNoVersion searchTable ncbiRefSeqPredicted query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]* dontCheck X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchTable ncbiRefSeqOther searchPriority 2.07207 searchType bigBed