bf7206d3cbaf92e2e3e29a3f1f966b1502d21b87 hiram Mon Jan 13 13:18:31 2020 -0800 now running up NCBI RefSeq track on assembly hubs refs #24748 diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh index 7944df4..47234f9 100755 --- src/hg/utils/automation/asmHubTrackDb.sh +++ src/hg/utils/automation/asmHubTrackDb.sh @@ -356,30 +356,168 @@ bigDataUrl bbi/%s.ncbiGene.bb type bigGenePred html html/%s.ncbiGene searchIndex name%s url https://www.ncbi.nlm.nih.gov/gene/?term=\$\$ urlLabel Entrez gene labelFields geneName,geneName2 group genes\n\n" "${asmId}" "${asmId}" "${searchTrix}" $scriptDir/asmHubNcbiGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.ncbiGene.html haveNcbiGene="yes" fi ################################################################### +# ncbiRefSeq composite track +if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeq.bb ]; then +rm -f $buildDir/bbi/${asmId}.ncbiRefSeq.bb +rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeq.ix +rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeq.ixx +ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.bb $buildDir/bbi/${asmId}.ncbiRefSeq.bb +ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.ix $buildDir/ixIxx/${asmId}.ncbiRefSeq.ix +ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeq.ixx + + printf "track refSeqComposite +compositeTrack on +shortLabel NCBI RefSeq +longLabel RefSeq gene predictions from NCBI +group genes +visibility pack +type bigBed +dragAndDrop subTracks +noInherit on +allButtonPair on +dataVersion html/ncbiRefSeqVersion.txt +html html/%s.refSeqComposite +priority 2 + + track ncbiRefSeq + parent refSeqComposite on + color 12,12,120 + altColor 120,12,12 + shortLabel RefSeq All + type bigGenePred + searchIndex name + searchTrix ixIxx/%s.ncbiRefSeq.ix + bigDataUrl bbi/%s.ncbiRefSeq.bb + 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\n\n" "${asmId}" "${asmId}" "${asmId}" + + if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb ]; then + rm -f $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx + + printf " track ncbiRefSeqCurated + color 12,12,120 + parent refSeqComposite on + shortLabel RefSeq Curated + longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) + type bigGenePred + searchIndex name + searchTrix ixIxx/%s.ncbiRefSeqCurated.ix + idXref ncbiRefSeqLink mrnaAcc name + bigDataUrl bbi/%s.ncbiRefSeqCurated.bb + baseColorUseCds given + baseColorDefault genomicCodons + priority 2\n\n" "${asmId}" "${asmId}" + fi + + if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb ]; then + rm -f $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx + + printf " track ncbiRefSeqPredicted + color 12,12,120 + parent refSeqComposite on + shortLabel RefSeq Predicted + longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) + type bigGenePred + searchIndex name + searchTrix ixIxx/%s.ncbiRefSeqPredicted.ix + idXref ncbiRefSeqLink mrnaAcc name + bigDataUrl bbi/%s.ncbiRefSeqPredicted.bb + baseColorUseCds given + baseColorDefault genomicCodons + priority 3\n\n" "${asmId}" "${asmId}" + fi + + if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb ]; then + rm -f $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ix + rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ixx + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb +rm -f $buildDir/ixIxx/${asmId}.xenoRefGene.ix + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ix + ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ixx + + printf " track ncbiRefSeqOther + color 32,32,32 + parent refSeqComposite on + shortLabel RefSeq Other + longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) + priority 4 + searchIndex name + searchTrix ixIxx/%s.ncbiRefSeqOther.ix + bigDataUrl bbi/%s.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/\$\$\" 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/\$\$\"\n\n" "${asmId}" "${asmId}" + + fi + + if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.bigPsl.bb ]; then + rm -f $buildDir/bbi/${asmId}.bigPsl.bb + ln -s ../trackData/ncbiRefSeq/$asmId.bigPsl.bb $buildDir/bbi/${asmId}.bigPsl.bb + + printf " track ncbiRefSeqPsl + priority 5 + parent refSeqComposite off + shortLabel RefSeq Alignments + longLabel RefSeq Alignments of RNAs + type bigPsl + bigDataUrl bbi/%s.bigPsl.bb + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsMaxZoom 10000.0 + showCdsAllScales . + baseColorDefault diffCodons + pslSequence no + baseColorUseSequence lfExtra + baseColorUseCds table given + color 0,0,0\n\n" "${asmId}" + fi + + $scriptDir/asmHubNcbiRefSeq.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.refSeqComposite.html + +fi # ncbiRefSeq composite track + +################################################################### # CpG Islands composite export cpgVis="off" # if there is no unmasked track, then set cpgVis to pack if [ ! -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb ]; then cpgVis="on" fi if [ -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb -o -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then rm -f ${buildDir}/bbi/${asmId}.cpgIslandExtUnmasked.bb ${buildDir}/bbi/${asmId}.cpgIslandExt.bb printf "track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility pack