d4ecfb99f3d657c23434e078924e18010ebfd5da ccpowell Thu Jul 18 15:48:58 2019 -0700 Remvoing refSeqCompositeHuman files because refSeqComposite is globally inherited, refs #23818 diff --git src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra deleted file mode 100644 index c613c7e..0000000 --- src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra +++ /dev/null @@ -1,200 +0,0 @@ -# Human refSeqComposite w/ YP_* accessions -include refSeqCompositeHuman.html - -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_*, and YP_*) - idXref ncbiRefSeqLink mrnaAcc name - baseColorUseCds given - priority 1 - - track ncbiRefSeqCurated - color 12,12,120 - parent refSeqComposite on - shortLabel RefSeq Curated - 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 refSeqComposite off - shortLabel RefSeq Predicted - longLabel NCBI RefSeq genes, predicted subset (XM_* and XR_*) - idXref ncbiRefSeqLink mrnaAcc name - baseColorUseCds given - priority 3 - - track ncbiRefSeqOther - color 32,32,32 - parent refSeqComposite off - shortLabel RefSeq Other - longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, 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 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 - trackHandler ncbiRefSeq - idXref ncbiRefSeqLink mrnaAcc name - color 20,20,160 - baseColorUseCds given - - 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 - - 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 - -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