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/mouse/refSeqComposite.mm10.mm39.ra src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra new file mode 100644 index 0000000..93931e7 --- /dev/null +++ src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra @@ -0,0 +1,206 @@ +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 off + 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 + 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 + + track ncbiRefSeqSelect + parent refSeqComposite off + priority 8 + type genePred + shortLabel RefSeq Select + longLabel NCBI RefSeq Select: One representative transcript per protein-coding gene + 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