3bfcaafa2a767e8885725db659a21c4ae33f1386 max Fri Jan 17 09:55:07 2020 -0800 changing ncbi refseq title a little, refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index 78ef904..5986dcc 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,217 +1,217 @@ track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq gene predictions from NCBI group genes visibility pack 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 sets (NM_*, XM_*, NR_*, XR_*, NP_* or 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/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" 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 ncbiRefSeqSelect parent refSeqComposite off priority 7 type genePred shortLabel RefSeq Select - longLabel NCBI RefSeq Select: representative transcripts, usually one per protein-coding gene + longLabel NCBI RefSeq Select & MANE: representative transcripts, usually one per protein-coding gene trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons track ncbiRefSeqHgmd parent refSeqComposite off priority 7 type genePred shortLabel RefSeq HGMD - longLabel Only NCBI RefSeq manually annotated transcripts with at least one HGMD clinical variant + longLabel NCBI RefSeq curated and annotated by HGMD, usually one per clinically relevant gene trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons track ncbiRefSeqMane parent refSeqComposite off priority 8 type genePred shortLabel RefSeq MANE longLabel RefSeq selected representative transcript for each gene, MANE 0.5 trackHandler ncbiRefSeq baseColorUseCds given baseColorDefault genomicCodons 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 9 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