2f106a9cd51707e6772b96064b2fcfc30bca95b0 ccpowell Thu Jul 18 14:54:51 2019 -0700 Switching YP with NP mention in all organism execept human, refs #23818 diff --git src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra new file mode 100644 index 0000000..6206dd3 --- /dev/null +++ src/hg/makeDb/trackDb/human/refSeqCompositeHuman.ra @@ -0,0 +1,200 @@ +# Human refSeqComposite w/ YP_* accessions +include refSeqCompositeHuman.ra + +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