4eac7e1d1e0aa730e53baa60c3b7437757ba7c6c lrnassar Thu Apr 11 15:01:34 2019 -0700 Fixing some refseq visilibity issues ref#22136 diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index a4070c8..1376c39 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,218 +1,219 @@ track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq gene predictions from NCBI group genes -visibility dense +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 ncbiRefSeqView shortLabel NCBI RefSeq genes and alignments view aNcbiRefSeq + visibility dense parent refSeqComposite on configurable on baseColorDefault genomicCodons track ncbiRefSeq parent ncbiRefSeqView off color 12,12,120 shortLabel RefSeq All subGroups view=aNcbiRefSeq longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, and YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given priority 1 track ncbiRefSeqCurated color 12,12,120 parent ncbiRefSeqView on shortLabel RefSeq Curated subGroups view=aNcbiRefSeq longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, and YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given priority 2 track ncbiRefSeqPredicted color 12,12,120 parent ncbiRefSeqView off shortLabel RefSeq Predicted subGroups view=aNcbiRefSeq longLabel NCBI RefSeq genes, predicted subset (XM_* and XR_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given priority 3 track ncbiRefSeqOther color 32,32,32 parent ncbiRefSeqView off shortLabel RefSeq Other subGroups view=aNcbiRefSeq longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, or YP_*) priority 4 searchIndex name,gene,ID,Name2,geneSynonym,product 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 ncbiRefSeqView off shortLabel RefSeq Alignments subGroups view=aNcbiRefSeq 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 subGroups view=aNcbiRefSeq priority 6 type bigBed 9 + skipEmptyFields on shortLabel RefSeq Diffs longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome parent ncbiRefSeqView off bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb itemRgb on track ncbiRefSeqHgmd subGroups view=aNcbiRefSeq priority 7 type genePred shortLabel RefSeq HGMD longLabel Only NCBI RefSeq manually annotated transcripts with at least one HGMD clinical variant parent ncbiRefSeqView off trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given track ncbiRefSeqMane subGroups view=aNcbiRefSeq priority 8 type genePred shortLabel RefSeq MANE longLabel RefSeq selected representative transcript for each gene, MANE 0.5 parent ncbiRefSeqView off trackHandler ncbiRefSeq track ucscRefSeqView parent refSeqComposite off shortLabel UCSC RefSeq Genes view zUcscRefSeq track refGene override parent ucscRefSeqView off shortLabel UCSC RefSeq longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*) subGroups view=zUcscRefSeq color 12,12,120 type genePred refPep refMrna idXref hgFixed.refLink mrnaAcc name dataVersion priority 6 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