0b81078213eff40174d357fbc8632ed7077baec4 braney Fri Aug 21 09:47:38 2020 -0700 changes to support the lack of native knownGene tables in an assembly. diff --git src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh index 28cd813..ccedd69 100644 --- src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh +++ src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh @@ -1,331 +1,332 @@ # This doc assumes that the gencode* tables have been built on $db db=hg38 GENCODE_VERSION=V35 dir=/hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build genomes=/hive/data/genomes tempDb=knownGeneV35 kent=$HOME/kent spDb=sp180404 cpuFarm=ku export curVer=13 mkdir -p $dir cd $dir echo "create database $tempDb" | hgsql "" echo "create table chromInfo like $db.chromInfo" | hgsql $tempDb echo "insert into chromInfo select * from $db.chromInfo" | hgsql $tempDb hgsql -e "select * from gencodeAnnot$GENCODE_VERSION" --skip-column-names $db | cut -f 2-16 | genePredToBed stdin stdout | sort -k1,1 -k2,2n | gzip -c > gencode${GENCODE_VERSION}.bed.gz touch oldToNew.tab zcat gencode${GENCODE_VERSION}.bed.gz > ucscGenes.bed txBedToGraph ucscGenes.bed ucscGenes ucscGenes.txg txgAnalyze ucscGenes.txg $genomes/$db/$db.2bit stdout | sort | uniq | bedClip stdin /cluster/data/hg38/chrom.sizes ucscSplice.bed zcat gencode${GENCODE_VERSION}.bed.gz | awk '{print $4}' | sort > newGencodeName.txt hgsql $db -Ne "select name,alignId from knownGene" | sort > oldGenToUcsc.txt kgAllocId oldGenToUcsc.txt newGencodeName.txt 5070122 stdout | sort -u > txToAcc.tab # lastId 5072896 makeUcscGeneTables -justKnown $db $tempDb $GENCODE_VERSION txToAcc.tab hgLoadSqlTab -notOnServer $tempDb knownGene $kent/src/hg/lib/knownGene.sql knownGene.gp hgLoadGenePred -genePredExt $tempDb knownGeneExt knownGeneExt.gp hgMapToGene -type=psl -all -tempDb=$tempDb $db all_mrna knownGene knownToMrna hgMapToGene -tempDb=$tempDb $db refGene knownGene knownToRefSeq hgMapToGene -type=psl -tempDb=$tempDb $db all_mrna knownGene knownToMrnaSingle makeUcscGeneTables $db $tempDb $GENCODE_VERSION txToAcc.tab hgLoadSqlTab -notOnServer $tempDb knownCanonical $kent/src/hg/lib/knownCanonical.sql knownCanonical.tab sort knownIsoforms.tab | uniq | hgLoadSqlTab -notOnServer $tempDb knownIsoforms $kent/src/hg/lib/knownIsoforms.sql stdin genePredToProt knownGeneExt.gp /cluster/data/$db/$db.2bit tmp.faa faFilter -uniq tmp.faa ucscGenes.faa hgPepPred $tempDb generic knownGenePep ucscGenes.faa hgLoadSqlTab -notOnServer $tempDb kgXref $kent/src/hg/lib/kgXref.sql kgXref.tab #ifdef NOTNOW # calculate score field with bitfields hgsql $db -Ne "select * from gencodeAnnot$GENCODE_VERSION" | cut -f 2- | sort > gencodeAnnot$GENCODE_VERSION.txt hgsql $db -Ne "select name,2 from gencodeAnnot$GENCODE_VERSION" | sort > knownCanon.txt hgsql $db -Ne "select * from gencodeTag$GENCODE_VERSION" | grep basic | sed 's/basic/1/' | sort > knownTag.txt hgsql $db -Ne "select transcriptId,transcriptClass from gencodeAttrs$GENCODE_VERSION where transcriptClass='pseudo'" | sed 's/pseudo/4/' > knownAttrs.txt sort knownCanon.txt knownTag.txt knownAttrs.txt | awk '{if ($1 != last) {print last, sum; sum=$2; last=$1} else {sum += $2; }} END {print last, sum}' | tail -n +2 > knownScore.txt #endif hgsql -e "select * from gencodeAnnot$GENCODE_VERSION" --skip-column-names $db | cut -f 2-16 | tawk '{print $1,$13,$14,$8,$15}' | sort | uniq > knownCds.tab hgLoadSqlTab -notOnServer $tempDb knownCds $kent/src/hg/lib/knownCds.sql knownCds.tab cat << __EOF__ > colors.sed s/coding/12\t12\t120/ s/nonCoding/0\t100\t0/ s/pseudo/255\t51\t255/ s/other/254\t0\t0/ __EOF__ hgsql $db -Ne "select * from gencodeAttrs$GENCODE_VERSION" | tawk '{print $4,$10}' | sed -f colors.sed > colors.txt #ifdef NOTNOW hgsql $db -Ne "select * from gencodeToUniProt$GENCODE_VERSION" | tawk '{print $1,$2}'| sort > uniProt.txt hgsql $db -Ne "select * from gencodeAnnot$GENCODE_VERSION" | tawk '{print $1,$12}' | sort > gene.txt join -a 1 gene.txt uniProt.txt > geneNames.txt #endif //genePredToBigGenePred -score=knownScore.txt -colors=colors.txt -geneNames=geneNames.txt -known gencodeAnnot$GENCODE_VERSION.txt gencodeAnnot$GENCODE_VERSION.bgpInput hgsql $db -Ne "select * from gencodeAnnot$GENCODE_VERSION" | cut -f 2- > gencodeAnnot$GENCODE_VERSION.txt #genePredToBigGenePred -colors=colors.txt gencodeAnnot$GENCODE_VERSION.txt stdout | sort -k1,1 -k2,2n > gencodeAnnot$GENCODE_VERSION.bgpInput hgsql $tempDb -Ne "select kgId, geneSymbol, spID from kgXref" > geneNames.txt #hgsql $tempDb -Ne "select * from knownCds" > knownCds.txt #genePredToBigGenePred -colors=colors.txt -known knownGene.gp stdout | sort -k1,1 -k2,2n > gencodeAnnot$GENCODE_VERSION.bgpInput genePredToBigGenePred -colors=colors.txt -geneNames=geneNames.txt -known -cds=knownCds.tab knownGene.gp stdout | sort -k1,1 -k2,2n > gencodeAnnot$GENCODE_VERSION.bgpInput tawk '{print $4,$0}' gencodeAnnot$GENCODE_VERSION.bgpInput | sort > join1 hgsql $db -Ne "select transcriptId, transcriptClass from gencodeAttrs$GENCODE_VERSION" | sort > attrs.txt join -t $'\t' join1 attrs.txt > join2 hgsql $db -Ne "select transcriptId, source from gencodeTranscriptSource$GENCODE_VERSION" | sort > source.txt join -t $'\t' join2 source.txt > join3 hgsql $db -Ne "select transcriptId, transcriptType from gencodeAttrs$GENCODE_VERSION" | sort > biotype.txt join -t $'\t' join3 biotype.txt > join4 hgsql $db -Ne "select transcriptId, tag from gencodeTag$GENCODE_VERSION" | sort | tawk '{if ($1 != last) {print last,buff; buff=$2}else {buff=buff "," $2} last=$1} END {print last,buff}' | tail -n +2 > tags.txt join -t $'\t' -a 1 -e"none" -o auto join4 tags.txt > join5 hgsql $db -Ne "select transcriptId, level from gencodeAttrs$GENCODE_VERSION" | sort > level.txt join -t $'\t' join5 level.txt > join6 grep basic tags.txt | tawk '{print $1, 1, "basic"}' > basic.txt tawk '{print $5,0,"canonical"}' knownCanonical.tab | sort > canonical.txt tawk '{print $4,2,"all"}' gencodeAnnot$GENCODE_VERSION.bgpInput | sort > all.txt sort -k1,1 -k2,2n basic.txt canonical.txt all.txt | tawk '{if ($1 != last) {print last,buff; buff=$3}else {buff=buff "," $3} last=$1} END {print last,buff}' | tail -n +2 > tier.txt join -t $'\t' join6 tier.txt > join7 cut -f 2- -d $'\t' join7 | sort -k1,1 -k2,2n > bgpInput.txt bedToBigBed -extraIndex=name -type=bed12+16 -tab -as=$HOME/kent/src/hg/lib/gencodeBGP.as bgpInput.txt /cluster/data/$db/chrom.sizes $db.gencode$GENCODE_VERSION.bb ln -s `pwd`/$db.gencode$GENCODE_VERSION.bb /gbdb/$db/gencode/gencode$GENCODE_VERSION.bb hgsql $tempDb -e "select * from knownToMrna" | tail -n +2 | tawk '{if ($1 != last) {print last, count, buffer; count=1; buffer=$2} else {count++;buffer=$2","buffer} last=$1}' | tail -n +2 | sort > tmp1 hgsql $tempDb -e "select * from knownToMrnaSingle" | tail -n +2 | sort > tmp2 join tmp2 tmp1 > knownGene.ev txGeneAlias $db $spDb kgXref.tab knownGene.ev oldToNew.tab foo.alias foo.protAlias tawk '{split($2,a,"."); for(ii = 1; ii <= a[2]; ii++) print $1,a[1] "." ii }' txToAcc.tab >> foo.alias +tawk '{split($1,a,"."); for(ii = 1; ii <= a[2] - 1; ii++) print $1,a[1] "." ii }' txToAcc.tab >> foo.alias sort foo.alias | uniq > ucscGenes.alias sort foo.protAlias | uniq > ucscGenes.protAlias rm foo.alias foo.protAlias hgLoadSqlTab -notOnServer $tempDb kgAlias $kent/src/hg/lib/kgAlias.sql ucscGenes.alias hgLoadSqlTab -notOnServer $tempDb kgProtAlias $kent/src/hg/lib/kgProtAlias.sql ucscGenes.protAlias hgsql --skip-column-names -e "select mrnaAcc,locusLinkId from hgFixed.refLink" $db > refToLl.txt hgMapToGene -tempDb=$tempDb $db refGene knownGene knownToLocusLink -lookup=refToLl.txt knownToVisiGene $tempDb -probesDb=$db hgMapToGene $db -tempDb=$tempDb -all -type=genePred gtexGeneModelV6 knownGene knownToGtex awk '{OFS="\t"} {print $4,$4}' ucscGenes.bed | sort | uniq > knownToEnsembl.tab cp knownToEnsembl.tab knownToGencode${GENCODE_VERSION}.tab hgLoadSqlTab -notOnServer $tempDb knownToEnsembl $kent/src/hg/lib/knownTo.sql knownToEnsembl.tab hgLoadSqlTab -notOnServer $tempDb knownToGencode${GENCODE_VERSION} $kent/src/hg/lib/knownTo.sql knownToGencode${GENCODE_VERSION}.tab # make knownToLynx mkdir -p $dir/lynx cd $dir/lynx wget "http://lynx.ci.uchicago.edu/downloads/LYNX_GENES.tab" awk '{print $2}' LYNX_GENES.tab | sort > lynxExists.txt hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $tempDb | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt join lynxExists.txt geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2,$1}' | sort > knownToLynx.tab hgLoadSqlTab -notOnServer $tempDb knownToLynx $kent/src/hg/lib/knownTo.sql knownToLynx.tab # load malacards table hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $tempDb | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt hgsql -e "select geneSymbol from malacards" --skip-column-names $db | sort > malacardExists.txt join malacardExists.txt geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2, $1}' > knownToMalacard.txt hgLoadSqlTab -notOnServer $tempDb knownToMalacards $kent/src/hg/lib/knownTo.sql knownToMalacard.txt twoBitToFa -noMask /cluster/data/$db/$db.2bit -bed=ucscGenes.bed stdout | faFilter -uniq stdin ucscGenes.fa hgPepPred $tempDb generic knownGeneMrna ucscGenes.fa hgMapToGene -tempDb=$tempDb $db gnfAtlas2 knownGene knownToGnfAtlas2 '-type=bed 12' hgMapToGene -tempDb=$tempDb $db affyU133 knownGene knownToU133 hgMapToGene -tempDb=$tempDb $db affyU95 knownGene knownToU95 hgsql $tempDb -Ne "create view all_mrna as select * from $db.all_mrna" hgsql $tempDb -Ne "create view ensGene as select * from $db.ensGene" hgsql $tempDb -Ne "create view gtexGene as select * from $db.gtexGene" hgsql $tempDb -Ne "create view gencodeAnnotV35 as select * from $db.gencodeAnnotV35" hgsql $tempDb -Ne "create view gencodeAttrsV35 as select * from $db.gencodeAttrsV35" hgsql $tempDb -Ne "create view gencodeGeneSourceV35 as select * from $db.gencodeGeneSourceV35" hgsql $tempDb -Ne "create view gencodeTranscriptSourceV35 as select * from $db.gencodeTranscriptSourceV35" hgsql $tempDb -Ne "create view gencodeToPdbV35 as select * from $db.gencodeToPdbV35" hgsql $tempDb -Ne "create view gencodeToPubMedV35 as select * from $db.gencodeToPubMedV35" hgsql $tempDb -Ne "create view gencodeToRefSeqV35 as select * from $db.gencodeToRefSeqV35" hgsql $tempDb -Ne "create view gencodeTagV35 as select * from $db.gencodeTagV35" hgsql $tempDb -Ne "create view gencodeTranscriptSupportV35 as select * from $db.gencodeTranscriptSupportV35" hgsql $tempDb -Ne "create view gencodeToUniProtV35 as select * from $db.gencodeToUniProtV35" bioCycDir=/hive/data/outside/bioCyc/190905/download/humancyc/21.0/data mkdir $dir/bioCyc cd $dir/bioCyc grep -E -v "^#" $bioCycDir/genes.col > genes.tab grep -E -v "^#" $bioCycDir/pathways.col | awk -F'\t' '{if (140 == NF) { printf "%s\t\t\n", $0; } else { print $0}}' > pathways.tab kgBioCyc1 -noEnsembl genes.tab pathways.tab $tempDb bioCycPathway.tab bioCycMapDesc.tab hgLoadSqlTab $tempDb bioCycPathway ~/kent/src/hg/lib/bioCycPathway.sql ./bioCycPathway.tab hgLoadSqlTab $tempDb bioCycMapDesc ~/kent/src/hg/lib/bioCycMapDesc.sql ./bioCycMapDesc.tab mkdir -p $dir/kegg cd $dir/kegg # Make the keggMapDesc table, which maps KEGG pathway IDs to descriptive names cp /cluster/data/hg19/bed/ucsc.14.3/kegg/map_title.tab . # wget --timestamping ftp://ftp.genome.jp/pub/kegg/pathway/map_title.tab cat map_title.tab | sed -e 's/\t/\thsa\t/' > j.tmp cut -f 2 j.tmp >j.hsa cut -f 1,3 j.tmp >j.1 paste j.hsa j.1 |sed -e 's/\t//' > keggMapDesc.tab rm j.hsa j.1 j.tmp hgLoadSqlTab -notOnServer $tempDb keggMapDesc $kent/src/hg/lib/keggMapDesc.sql keggMapDesc.tab # Following in two-step process, build/load a table that maps UCSC Gene IDs # to LocusLink IDs and to KEGG pathways. First, make a table that maps # LocusLink IDs to KEGG pathways from the downloaded data. Store it temporarily # in the keggPathway table, overloading the schema. cp /cluster/data/hg19/bed/ucsc.14.3/kegg/hsa_pathway.list . cat hsa_pathway.list| sed -e 's/path://'|sed -e 's/:/\t/' > j.tmp hgLoadSqlTab -notOnServer $tempDb keggPathway $kent/src/hg/lib/keggPathway.sql j.tmp # Next, use the temporary contents of the keggPathway table to join with # knownToLocusLink, creating the real content of the keggPathway table. # Load this data, erasing the old temporary content hgsql $tempDb -B -N -e 'select distinct name, locusID, mapID from keggPathway p, knownToLocusLink l where p.locusID=l.value' > keggPathway.tab hgLoadSqlTab -notOnServer $tempDb \ keggPathway $kent/src/hg/lib/keggPathway.sql keggPathway.tab # Finally, update the knownToKeggEntrez table from the keggPathway table. hgsql $tempDb -B -N -e 'select kgId, mapID, mapID, "+", locusID from keggPathway' |sort -u| sed -e 's/\t+\t/+/' > knownToKeggEntrez.tab hgLoadSqlTab -notOnServer $tempDb knownToKeggEntrez $kent/src/hg/lib/knownToKeggEntrez.sql knownToKeggEntrez.tab #hgsql $tempDb -e "delete k from knownToKeggEntrez k, kgXref x where k.name = x.kgID and x.geneSymbol = 'abParts'" # Make spMrna table cd $dir #hgsql $db -N -e "select spDisplayID,kgID from kgXref where spDisplayID != ''" > spMrna.tab; hgsql $tempDb -N -e "select spDisplayID,kgID from kgXref where spDisplayID != ''" > spMrna.tab; hgLoadSqlTab $tempDb spMrna $kent/src/hg/lib/spMrna.sql spMrna.tab # Do CGAP tables mkdir -p $dir/cgap cd $dir/cgap wget --timestamping -O Hs_GeneData.dat "ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat" hgCGAP Hs_GeneData.dat cat cgapSEQUENCE.tab cgapSYMBOL.tab cgapALIAS.tab|sort -u > cgapAlias.tab hgLoadSqlTab -notOnServer $tempDb cgapAlias $kent/src/hg/lib/cgapAlias.sql ./cgapAlias.tab hgLoadSqlTab -notOnServer $tempDb cgapBiocPathway $kent/src/hg/lib/cgapBiocPathway.sql ./cgapBIOCARTA.tab cat cgapBIOCARTAdesc.tab|sort -u > cgapBIOCARTAdescSorted.tab hgLoadSqlTab -notOnServer $tempDb cgapBiocDesc $kent/src/hg/lib/cgapBiocDesc.sql cgapBIOCARTAdescSorted.tab # MAKE FOLDUTR TABLES # First set up directory structure and extract UTR sequence on hgwdev cd $dir mkdir -p rnaStruct cd rnaStruct ln -s /cluster/data/$db/$db.2bit $tempDb.2bit mkdir -p utr3/split utr5/split utr3/fold utr5/fold # these commands take some significant time utrFa -nibPath=`pwd` $tempDb knownGene utr3 utr3/utr.fa utrFa -nibPath=`pwd` $tempDb knownGene utr5 utr5/utr.fa # Split up files and make files that define job. faSplit sequence utr3/utr.fa 10000 utr3/split/s faSplit sequence utr5/utr.fa 10000 utr5/split/s ls -1 utr3/split > utr3/in.lst ls -1 utr5/split > utr5/in.lst cd utr3 cat << _EOF_ > template #LOOP rnaFoldBig split/\$(path1) fold #ENDLOOP _EOF_ gensub2 in.lst single template jobList cp template ../utr5 cd ../utr5 gensub2 in.lst single template jobList # Do cluster runs for UTRs ssh $cpuFarm "cd $dir/rnaStruct/utr3; para make jobList" ssh $cpuFarm "cd $dir/rnaStruct/utr5; para make jobList" ssh $cpuFarm "cd $dir/rnaStruct/utr3; para time" ssh $cpuFarm "cd $dir/rnaStruct/utr5; para time" # Load database cd $dir/rnaStruct/utr5 hgLoadRnaFold $tempDb foldUtr5 fold cd ../utr3 hgLoadRnaFold -warnEmpty $tempDb foldUtr3 fold # Clean up rm -r split fold err batch.bak cd ../utr5 rm -r split fold err batch.bak hgKgGetText $tempDb tempSearch.txt sort tempSearch.txt > tempSearch2.txt tawk '{split($2,a,"."); printf "%s\t", $1;for(ii = 1; ii <= a[2]; ii++) printf "%s ",a[1] "." ii; printf "\n" }' txToAcc.tab | sort > tempSearch3.txt join tempSearch2.txt tempSearch3.txt | sort > knownGene.txt ixIxx knownGene.txt knownGene${GENCODE_VERSION}.ix knownGene${GENCODE_VERSION}.ixx rm -rf /gbdb/$db/knownGene${GENCODE_VERSION}.ix /gbdb/$db/knownGene${GENCODE_VERSION}.ixx ln -s $dir/knownGene${GENCODE_VERSION}.ix /gbdb/$db/knownGene${GENCODE_VERSION}.ix ln -s $dir/knownGene${GENCODE_VERSION}.ixx /gbdb/$db/knownGene${GENCODE_VERSION}.ixx #zcat gencode${GENCODE_VERSION}.bed.gz > ucscGenes.bed #jtwoBitToFa -noMask /cluster/data/$db/$db.2bit -bed=ucscGenes.bed stdout | faFilter -uniq stdin ucscGenes.fa #jhgPepPred $tempDb generic knownGeneMrna ucscGenes.fa bedToPsl /cluster/data/$db/chrom.sizes ucscGenes.bed ucscGenes.psl pslRecalcMatch ucscGenes.psl /cluster/data/$db/$db.2bit ucscGenes.fa kgTargetAli.psl # should be zero awk '$11 != $1 + $3+$4' kgTargetAli.psl hgLoadPsl $tempDb kgTargetAli.psl cd $dir # Make PCR target for UCSC Genes, Part 1. # 1. Get a set of IDs that consist of the UCSC Gene accession concatenated with the # gene symbol, e.g. uc010nxr.1__DDX11L1 hgsql $tempDb -N -e 'select kgId,geneSymbol from kgXref' \ | perl -wpe 's/^(\S+)\t(\S+)/$1\t${1}__$2/ || die;' \ | sort -u > idSub.txt # 2. Get a file of per-transcript fasta sequences that contain the sequences of each UCSC Genes transcript, with this new ID in the place of the UCSC Genes accession. Convert that file to TwoBit format and soft-link it into /gbdb/hg38/targetDb/ awk '{if (!found[$4]) print; found[$4]=1 }' ucscGenes.bed > nodups.bed subColumn 4 nodups.bed idSub.txt ucscGenesIdSubbed.bed sequenceForBed -keepName -db=$db -bedIn=ucscGenesIdSubbed.bed -fastaOut=stdout | faToTwoBit stdin ${db}KgSeq${curVer}.2bit mkdir -p /gbdb/$db/targetDb/ rm -f /gbdb/$db/targetDb/${db}KgSeq${curVer}.2bit ln -s $dir/${db}KgSeq${curVer}.2bit /gbdb/$db/targetDb/ # Load the table kgTargetAli, which shows where in the genome these targets are. cut -f 1-10 knownGene.gp | genePredToFakePsl $tempDb stdin kgTargetAli.psl /dev/null hgLoadPsl $tempDb kgTargetAli.psl # 3. Ask cluster-admin to start an untranslated, -stepSize=5 gfServer on # /gbdb/$db/targetDb/${db}KgSeq${curVer}.2bit # 4. On hgwdev, insert new records into blatServers and targetDb, using the # host (field 2) and port (field 3) specified by cluster-admin. Identify the # blatServer by the keyword "$db"Kg with the version number appended # untrans gfServer for hg38KgSeq12 on host blat1b, port 17897 hgsql hgcentraltest -e \ 'INSERT into blatServers values ("hg38KgSeq13", "blat1b", 1909, 0, 1);' hgsql hgcentraltest -e \ 'INSERT into targetDb values("hg38KgSeq13", "GENCODE Genes", \ "hg38", "knownGeneV35.kgTargetAli", "", "", \ "/gbdb/hg38/targetDb/hg38KgSeq13.2bit", 1, now(), "");'