287b19c93b42f39fec456fd6733be92b78818215 max Wed Jul 3 02:25:40 2019 -0700 removing ncbi refseq views, as per Jim and Brian Lee, no redmine (yet) diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index 1376c39..6bb6df7 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,152 +1,130 @@ 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 +#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 + parent refSeqComposite 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 + parent refSeqComposite 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 + parent refSeqComposite 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 + parent refSeqComposite 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 + 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 ncbiRefSeqView off + parent refSeqComposite 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 + parent refSeqComposite off 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 + parent refSeqComposite off 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 + parent refSeqComposite off 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 + parent refSeqComposite 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 + priority 9 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