export dir=/cluster/data/hg38/bed/ucsc.16.5 export GENCODE_VERSION=V22 export oldGeneDir=/cluster/data/hg38/bed/ucsc.15.1 export oldGeneBed=$oldGeneDir/ucscGenes.bed export db=hg38 export spDb=sp150225 export taxon=9606 export tempDb=tmpFoo67 export kent=$HOME/kent export lastVer=8 export curVer=9 export Db=Hg38 export xdb=mm10 export Xdb=Mm10 export ydb=canFam3 export zdb=rheMac3 export ratDb=rn4 export RatDb=Rn4 export fishDb=danRer7 export flyDb=dm3 export wormDb=ce6 export yeastDb=sacCer3 export tempFa=$dir/ucscGenes.faa export genomes=/hive/data/genomes export xdbFa=$genomes/$xdb/bed/ucsc.13.1/ucscGenes.faa export ratFa=$genomes/$ratDb/bed/blastpRgdGene2/rgdGene2Pep.faa export fishFa=$genomes/$fishDb/bed/blastp/ensembl.faa export flyFa=$genomes/$flyDb/bed/hgNearBlastp/100806/$flyDb.flyBasePep.faa export wormFa=$genomes/$wormDb/bed/blastp/wormPep190.faa export yeastFa=$genomes/$yeastDb/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa export scratchDir=/hive/users/braney/scratch export blastTab=hgBlastTab export xBlastTab=mmBlastTab export rnBlastTab=rnBlastTab export dbHost=hgwdev export ramFarm=ku export cpuFarm=ku mkdir -p $dir cd $dir echo "create database $tempDb" | hgsql "" echo "create table knownGeneOld$lastVer like $db.knownGene" | hgsql $tempDb echo "insert into knownGeneOld$lastVer select * from $db.knownGene" | hgsql $tempDb echo "create table kgXrefOld$lastVer like $db.kgXref" | hgsql $tempDb echo "insert into kgXrefOld$lastVer select * from $db.kgXref" | hgsql $tempDb hgsql -e "select * from wgEncodeGencodeComp$GENCODE_VERSION" --skip-column-names hg38 | cut -f 2-16 | genePredToBed stdin stdout | tawk '{$4=$4 "." $1; print}' | gzip -c > gencode${GENCODE_VERSION}Comp.bed.gz #TODO: figure out better wayto deal with txLastId cp ~kent/src/hg/txGene/txGeneAccession/txLastId startId txGeneAccession -test $oldGeneBed ~kent/src/hg/txGene/txGeneAccession/txLastId gencode${GENCODE_VERSION}Comp.bed.gz txToAcc.tab oldToNew.tab tawk '{print $4}' oldToNew.tab | sort | uniq -c # 43681 compatible # 9459 exact # 51038 lost # 142038 new # check to make sure we don't have any dups. These two numbers should # be the same. awk '{print $2}' txToAcc.tab | sed 's/\..*//' | sort -u | wc -l # 195178 awk '{print $2}' txToAcc.tab | sed 's/\..*//' | sort | wc -l # 195178 # this should be the current db instead of olDdb if not the first release echo "select * from knownGene" | hgsql $db | sort > $db.knownGene.gp echo "create table knownGeneOld${lastVer} select * from hg38.knownGene" | hgsql $tempDb grep lost oldToNew.tab | awk '{print $2}' | sort > lost.txt join lost.txt $db.knownGene.gp > $db.lost.gp awk '{if ($7 == $6) print}' $db.lost.gp | wc -l # non-coding 27206 awk '{if ($7 != $6) print}' $db.lost.gp | wc -l # coding 23832 # Assign permanent accessions to each transcript, and make up a number # of our files with this accession in place of the temporary IDs we've been # using. Takes 4 seconds cd $dir cp ~kent/src/hg/txGene/txGeneAccession/txLastId saveLastId txGeneAccession $oldGeneBed saveLastId gencode${GENCODE_VERSION}Comp.bed.gz txToAcc.tab oldToNew.tab subColumn 4 gencode${GENCODE_VERSION}Comp.bed.gz txToAcc.tab ucscGenes.bed twoBitToFa /cluster/data/$db/$db.2bit -bed=ucscGenes.bed ucscGenes.fa bedToPsl /cluster/data/hg38/chrom.sizes ucscGenes.bed ucscGenes.psl pslRecalcMatch ucscGenes.psl /cluster/data/$db/$db.2bit ucscGenes.fa kgTargetAli.psl # should be zero awk '$11 != $1 + $3+$4' kgTargetAli.psl hgLoadPsl $tempDb kgTargetAli.psl getRnaPred -peptides $tempDb knownGene all ucscGenes.faa hgPepPred $tempDb generic knownGenePep ucscGenes.faa txBedToGraph ucscGenes.bed ucscGenes ucscGenes.txg txgAnalyze ucscGenes.txg $genomes/$db/$db.2bit stdout | sort | uniq > ucscSplice.bed hgLoadBed $tempDb knownAlt ucscSplice.bed #hgsql -N $spDb -e "select p.acc, p.val from protein p, accToTaxon x where x.taxon=$taxon and p.acc=x.acc" | awk '{print ">" $1;print $2}' >uniProt.fa #faSize uniProt.fa #needs two passes. First make knownGene, then supporting tables makeGencodeKnownGene -justKnown $db $tempDb $GENCODE_VERSION txToAcc.tab hgLoadSqlTab -notOnServer $tempDb knownGene $kent/src/hg/lib/knownGene.sql knownGene.gp hgMapToGene -all -tempDb=$tempDb $db all_mrna knownGene knownToMrna hgMapToGene -tempDb=$tempDb $db refGene knownGene knownToRefSeq hgMapToGene -tempDb=$tempDb $db all_mrna knownGene knownToMrnaSingle makeGencodeKnownGene $db $tempDb $GENCODE_VERSION txToAcc.tab hgLoadSqlTab -notOnServer $tempDb kgColor $kent/src/hg/lib/kgColor.sql kgColor.tab hgLoadSqlTab -notOnServer $tempDb knownIsoforms $kent/src/hg/lib/knownIsoforms.sql knownIsoforms.tab hgLoadSqlTab -notOnServer $tempDb kgXref $kent/src/hg/lib/kgXref.sql kgXref.tab hgLoadSqlTab -notOnServer $tempDb knownCanonical $kent/src/hg/lib/knownCanonical.sql knownCanonical.tab 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 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 # Build kgSpAlias table, which combines content of both kgAlias and kgProtAlias tables. hgsql $tempDb -N -e 'select kgXref.kgID, spID, alias from kgXref, kgAlias where kgXref.kgID=kgAlias.kgID' > kgSpAlias_0.tmp hgsql $tempDb -N -e 'select kgXref.kgID, spID, alias from kgXref, kgProtAlias where kgXref.kgID=kgProtAlias.kgID' >> kgSpAlias_0.tmp cat kgSpAlias_0.tmp|sort -u > kgSpAlias.tab rm kgSpAlias_0.tmp hgLoadSqlTab -notOnServer $tempDb kgSpAlias $kent/src/hg/lib/kgSpAlias.sql kgSpAlias.tab txGeneExplainUpdate2 $oldGeneBed ucscGenes.bed kgOldToNew.tab hgLoadSqlTab -notOnServer $tempDb kg${lastVer}ToKg${curVer} $kent/src/hg/lib/kg1ToKg2.sql kgOldToNew.tab # add kg${lastVer}ToKg${curVer} to all.joiner !!!! # fake kgColor #tawk '{print $1, 0, 0, 0}' knownGene.gp > knownGene.color #hgLoadSqlTab -notOnServer $tempDb kgColor $kent/src/hg/lib/kgColor.sql knownGene.color sort txToAcc.tab > tmp1 hgsql -e "select * from wgEncodeGencodeComp$GENCODE_VERSION" --skip-column-names hg38 | cut -f 2-16 | tawk '{print $1 "." $2,$13,$14,$8,$15}' | sort | join /dev/stdin tmp1 | awk 'BEGIN {OFS="\t"} {print $6, $2, $3, $4, $5}' | sort > knownCds.tab hgLoadSqlTab -notOnServer $tempDb knownCds $kent/src/hg/lib/knownCds.sql knownCds.tab sed 's/\.chr.*\t/\t/' txToAcc.tab | sort > tmp1 hgsql -e "select * from wgEncodeGencodeTag$GENCODE_VERSION" --skip-column-names hg38 | subColumn 1 stdin tmp1 stdout -miss=missedTags.txt | grep -v "^ENS" | sort > knownToTag.tab hgLoadSqlTab -notOnServer $tempDb knownToTag $kent/src/hg/lib/knownTo.sql knownToTag.tab #zcat /cluster/data/hg38/bed/gencodeV22/data/release_22/gencode.v22.pc_translations.fa.gz | sed 's/.*ENST/>ENST/' | sed 's/|.*//' | tawk '/>/ {name=$1} ! />/ {print name, $0}' | tr -d '>' |sort > tmp11 #join tmp11 tmp1 | awk '{printf ">%s\n%s\n",$3,$2}' > ucscGenes.faa # this is missing the PAR genes #hgPepPred $tempDb generic knownGenePep ucscGenes.faa #zcat /cluster/data/hg38/bed/gencodeV22/data/release_22/gencode.v22.pc_transcripts.fa.gz | sed 's/.*ENST/>ENST/' | sed 's/|.*//' | awk '/>/ {name=$1} ! />/ {print name, $0}' | tr -d '>' |sort > tmp12 #join tmp12 tmp1 | awk '{printf ">%s\n%s\n",$3,$2}' > ucscGenes.fa #hgPepPred $tempDb generic knownGeneMrna ucscGenes.fa hgKgGetText $tempDb knownGene.text ixIxx knownGene.text knownGene.ix knownGene.ixx rm -rf /gbdb/$tempDb/knownGene.ix /gbdb/$tempDb/knownGene.ixx ln -s $dir/knownGene.ix /gbdb/$tempDb/knownGene.ix ln -s $dir/knownGene.ixx /gbdb/$tempDb/knownGene.ixx hgsql --skip-column-names -e "select mrnaAcc,locusLinkId from refLink" $db > refToLl.txt hgMapToGene -tempDb=$tempDb $db refGene knownGene knownToLocusLink -lookup=refToLl.txt knownToVisiGene $tempDb -probesDb=$db #touch empty.ev #/cluster/home/braney/bin/x86_64/txGeneAlias hg19 uniProt kgXref.tab empty.ev oldToNew.tab alias.tab proAlias.tab #sort alias.tab | uniq > kgAlias.tab #sort proAlias.tab | uniq > kgProtAlias.tab tawk '{print $2,$1}' tmp1 | sort > knownToEnsembl.tab tawk '{print $2,$1}' tmp1 | sort > knownToGencode${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 hgMapToGene -tempDb=$tempDb $db gnfAtlas2 knownGene knownToGnfAtlas2 '-type=bed 12' # start not done # Make up and load kgColor table. Takes about a minute. $txGeneColor $spDb ucscGenes.info ucscGenes.picks ucscGenes.color $hgLoadSqlTab -notOnServer $tempDb kgColor $kent/src/hg/lib/kgColor.sql ucscGenes.color # Load up kgProtMap2 table that says where exons are in terms of CDS $txGeneCdsMap weeded.bed weeded.info pick.picks refTweaked.psl \ refToPep.tab $genomes/$db/chrom.sizes cdsToRna.psl \ rnaToGenome.psl # Missed 337 of 40856 refSeq protein mappings. A small number of RefSeqs just map to genome in the UTR. $pslMap cdsToRna.psl rnaToGenome.psl cdsToGenome.psl $hgLoadPsl $tempDb ucscProtMap.psl -table=kgProtMap2 # TODO: Create knownToTreefam table. $mkdir -p $dir/treeFam $cd $dir/treeFam $wget "http://www.treefam.org/static/download/treefam_family_data.tar.gz" $tar xfz treefam_family_data.tar.gz $cd treefam_family_data $egrep -a ">ENSP[0-9]+" * | cut -d/ -f2 | tr -d : | sed -e 's/.aa.fasta//' |sed -e 's/.cds.fasta//' | grep -v accession | grep -v ^\> | tr '>' '\t' | tawk '{print $2,$1}' > ../ensToTreefam.tab $cd .. # hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db ensGene knownGene knownToEnsembl -noLoad #awk '{print $2,$1}' ../knownToEnsembl.tab | sort | uniq > ensTransUcsc.tab $hgsql $db -e "select value,name from knownToEnsembl" | sort | uniq > ensTransUcsc.tab $echo "select transcript,protein from ensGtp" | hgsql hg38 | sort | uniq | awk '{if (NF==2) print}' > ensTransProt.tab $join ensTransUcsc.tab ensTransProt.tab | awk '{if (NF==3)print $3, $2}' | sort | uniq > ensProtToUc.tab $join ensProtToUc.tab ensToTreefam.tab | sort -u | awk 'BEGIN {OFS="\t"} {print $2,$3}' | sort -u > knownToTreefam.tab $hgLoadSqlTab $tempDb knownToTreefam $kent/src/hg/lib/knownTo.sql knownToTreefam.tab #end not done if ($db =~ hg*) then # TODO #hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db HInvGeneMrna knownGene knownToHInv #hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db affyU133Plus2 knownGene knownToU133Plus2 hgMapToGene -tempDb=$tempDb $db affyU133 knownGene knownToU133 hgMapToGene -tempDb=$tempDb $db affyU95 knownGene knownToU95 mkdir hprd cd hprd wget "http://www.hprd.org/edownload/HPRD_FLAT_FILES_041310" tar xvf HPRD_FLAT_FILES_041310 knownToHprd $tempDb FLAT_FILES_072010/HPRD_ID_MAPPINGS.txt # hgsql $tempDb -e "delete k from knownToHprd k, kgXref x where k.name = x.kgID and x.geneSymbol = 'abParts'" endif if ($db =~ hg*) then cd $dir time hgExpDistance $tempDb hgFixed.gnfHumanU95MedianRatio \ hgFixed.gnfHumanU95Exps gnfU95Distance -lookup=knownToU95 time hgExpDistance $tempDb hgFixed.gnfHumanAtlas2MedianRatio \ hgFixed.gnfHumanAtlas2MedianExps gnfAtlas2Distance \ -lookup=knownToGnfAtlas2 endif if ($db =~ mm*) then hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db affyGnf1m knownGene knownToGnf1m hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db gnfAtlas2 knownGene knownToGnfAtlas2 '-type=bed 12' hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db affyU74 knownGene knownToU74 hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db affyMOE430 knownGene knownToMOE430 hgMapToGene -exclude=abGenes.txt -tempDb=$tempDb $db affyMOE430 -prefix=A: knownGene knownToMOE430A hgExpDistance $tempDb $db.affyGnfU74A affyGnfU74AExps affyGnfU74ADistance -lookup=knownToU74 hgExpDistance $tempDb $db.affyGnfU74B affyGnfU74BExps affyGnfU74BDistance -lookup=knownToU74 hgExpDistance $tempDb $db.affyGnfU74C affyGnfU74CExps affyGnfU74CDistance -lookup=knownToU74 hgExpDistance $tempDb hgFixed.gnfMouseAtlas2MedianRatio \ hgFixed.gnfMouseAtlas2MedianExps gnfAtlas2Distance -lookup=knownToGnf1m endif cd $dir # Create Human P2P protein-interaction Gene Sorter columns if ($db =~ hg*) then hgLoadNetDist $genomes/hg19/p2p/hprd/hprd.pathLengths $tempDb humanHprdP2P \ -sqlRemap="select distinct value, name from knownToHprd" hgLoadNetDist $genomes/hg19/p2p/vidal/humanVidal.pathLengths $tempDb humanVidalP2P -sqlRemap="select distinct locusLinkID, kgID from $db.refLink,kgXref where $db.refLink.mrnaAcc = kgXref.refSeq" hgLoadNetDist $genomes/hg19/p2p/wanker/humanWanker.pathLengths $tempDb humanWankerP2P -sqlRemap="select distinct locusLinkID, kgID from $db.refLink,kgXref where $db.refLink.mrnaAcc = kgXref.refSeq" endif # Run nice Perl script to make all protein blast runs for # Gene Sorter and Known Genes details page. Takes about # 45 minutes to run. rm -rf $dir/hgNearBlastp mkdir $dir/hgNearBlastp cd $dir/hgNearBlastp tcsh cat << _EOF_ > config.ra # Latest human vs. other Gene Sorter orgs: # mouse, rat, zebrafish, worm, yeast, fly targetGenesetPrefix known targetDb $tempDb queryDbs $xdb $ratDb $fishDb $flyDb $wormDb $yeastDb ${tempDb}Fa $tempFa ${xdb}Fa $xdbFa ${ratDb}Fa $ratFa ${fishDb}Fa $fishFa ${flyDb}Fa $flyFa ${wormDb}Fa $wormFa ${yeastDb}Fa $yeastFa buildDir $dir/hgNearBlastp scratchDir $scratchDir/brHgNearBlastp _EOF_ # exit tcsh rm -rf $scratchDir/brHgNearBlastp doHgNearBlastp.pl -noLoad -clusterHub=ku -distrHost=hgwdev -dbHost=hgwdev -workhorse=hgwdev config.ra > do.log 2>&1 & # Load self cd $dir/hgNearBlastp/run.$tempDb.$tempDb ./loadPairwise.csh # Load mouse and rat cd $dir/hgNearBlastp/run.$tempDb.$xdb hgLoadBlastTab $tempDb $xBlastTab -maxPer=1 out/*.tab cd $dir/hgNearBlastp/run.$tempDb.$ratDb hgLoadBlastTab $tempDb $rnBlastTab -maxPer=1 out/*.tab # Remove non-syntenic hits for mouse and rat # Takes a few minutes # TODO stopped here... need hg38 to rn4 mkdir -p /gbdb/$tempDb/liftOver rm -f /gbdb/$tempDb/liftOver/${tempDb}To$RatDb.over.chain.gz /gbdb/$tempDb/liftOver/${tempDb}To$Xdb.over.chain.gz ln -s $genomes/$db/bed/liftOver/${db}To$RatDb.over.chain.gz \ /gbdb/$tempDb/liftOver/${tempDb}To$RatDb.over.chain.gz ln -s $genomes/$db/bed/liftOver/${db}To${Xdb}.over.chain.gz \ /gbdb/$tempDb/liftOver/${tempDb}To$Xdb.over.chain.gz # delete non-syntenic genes from rat and mouse blastp tables cd $dir/hgNearBlastp synBlastp.csh $tempDb $xdb #old number of unique query values: 87304 #old number of unique target values 23890 #new number of unique query values: 82325 #new number of unique target values 23319 export oldDb=hg19 hgsql -e "select count(*) from mmBlastTab\G" $oldDb | tail -n +2 # count(*): 66798 hgsql -e "select count(*) from mmBlastTab\G" $tempDb | tail -n +2 # count(*): 82325 synBlastp.csh $tempDb $ratDb knownGene rgdGene2 # old number of unique query values: 75074 # old number of unique target values 10176 # new number of unique query values: 40867 # new number of unique target values 7693 hgsql -e "select count(*) from rnBlastTab\G" $oldDb | tail -n +2 # count(*): 28372 hgsql -e "select count(*) from rnBlastTab\G" $tempDb | tail -n +2 # count(*): 40867 # Make reciprocal best subset for the blastp pairs that are too # Far for synteny to help # Us vs. fish cd $dir/hgNearBlastp export aToB=run.$tempDb.$fishDb export bToA=run.$fishDb.$tempDb cat $aToB/out/*.tab > $aToB/all.tab cat $bToA/out/*.tab > $bToA/all.tab blastRecipBest $aToB/all.tab $bToA/all.tab $aToB/recipBest.tab $bToA/recipBest.tab hgLoadBlastTab $tempDb drBlastTab $aToB/recipBest.tab hgsql -e "select count(*) from drBlastTab\G" $oldDb | tail -n +2 # count(*): 13111 hgsql -e "select count(*) from drBlastTab\G" $tempDb | tail -n +2 # count(*): 13113 # Us vs. fly cd $dir/hgNearBlastp export aToB=run.$tempDb.$flyDb export bToA=run.$flyDb.$tempDb cat $aToB/out/*.tab > $aToB/all.tab cat $bToA/out/*.tab > $bToA/all.tab blastRecipBest $aToB/all.tab $bToA/all.tab $aToB/recipBest.tab $bToA/recipBest.tab hgLoadBlastTab $tempDb dmBlastTab $aToB/recipBest.tab hgsql -e "select count(*) from dmBlastTab\G" $oldDb | tail -n +2 # count(*): 5975 hgsql -e "select count(*) from dmBlastTab\G" $tempDb | tail -n +2 # count(*): 5987 # Us vs. worm cd $dir/hgNearBlastp export aToB=run.$tempDb.$wormDb export bToA=run.$wormDb.$tempDb cat $aToB/out/*.tab > $aToB/all.tab cat $bToA/out/*.tab > $bToA/all.tab blastRecipBest $aToB/all.tab $bToA/all.tab $aToB/recipBest.tab $bToA/recipBest.tab hgLoadBlastTab $tempDb ceBlastTab $aToB/recipBest.tab hgsql -e "select count(*) from ceBlastTab\G" $oldDb | tail -n +2 # count(*): 4948 hgsql -e "select count(*) from ceBlastTab\G" $tempDb | tail -n +2 # count(*): 4950 # Us vs. yeast cd $dir/hgNearBlastp export aToB=run.$tempDb.$yeastDb export bToA=run.$yeastDb.$tempDb cat $aToB/out/*.tab > $aToB/all.tab cat $bToA/out/*.tab > $bToA/all.tab blastRecipBest $aToB/all.tab $bToA/all.tab $aToB/recipBest.tab $bToA/recipBest.tab hgLoadBlastTab $tempDb scBlastTab $aToB/recipBest.tab hgsql -e "select count(*) from scBlastTab\G" $oldDb | tail -n +2 # count(*): 2365 hgsql -e "select count(*) from scBlastTab\G" $tempDb | tail -n +2 # count(*): 2378 # Clean up cd $dir/hgNearBlastp cat run.$tempDb.$tempDb/out/*.tab | gzip -c > run.$tempDb.$tempDb/all.tab.gz gzip run.*/all.tab #end didn't do # load malacards table hgsql hg38 -e 'drop table malacards; create table malacards (geneSymbol varchar(255), maladySymbol varchar(255), urlSuffix varchar(255), mainName varchar(255), geneScore float, diseaseScore float, isElite bool)' hgsql hg38 -e 'create index malacardsGeneIdx on malacards(geneSymbol);' s='"'; hgsql hg38 -e "delete from malacards; load data local infile 'Disease_Gene_Centric_dump_MC_v102.csv' into table malacards columns terminated by ',' enclosed by '$s' escaped by '' ignore 1 lines" # got this table by email from Noa Rappaport, see redmine 14417 # 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 hg38 | 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 # make knownToNextProt mkdir -p $dir/nextProt cd $dir/nextProt wget "ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt" awk '{print $0, $0}' nextprot_ac_list_all.txt | sed 's/NX_//' | sort > displayIdToNextProt.txt hgsql -e "select spID,kgId from kgXref" --skip-column-names hg38 | awk '{if (NF == 2) print}' | sort > displayIdToKgId.txt join displayIdToKgId.txt displayIdToNextProt.txt | awk 'BEGIN {OFS="\t"} {print $2,$3}' > knownToNextProt.tab hgLoadSqlTab -notOnServer $tempDb knownToNextProt $kent/src/hg/lib/knownTo.sql knownToNextProt.tab # make knownToWikipedia # TODO didn't doneeds a refresh...probably using Entrez. mkdir -p $dir/wikipedia cd $dir/wikipedia hgsql hg19 -e "select * from knownToWikipedia" | tail -n +2 | sort > oldKnownToWikipedia.tab hgsql hg38 -e "select oldId,newId from kg7ToKg8" | tail -n +2 | sort > kg7ToKg8.tab join kg7ToKg8.tab oldKnownToWikipedia.tab | awk 'BEGIN {OFS="\t"} {print $2,$3}' | sort | uniq | awk '{if ((NF == 2) && (haveSeen[$1] == 0)) print;haveSeen[$1]=1}' > knownToWikipedia.tab hgLoadSqlTab $tempDb knownToWikipedia $kent/src/hg/lib/knownToWikipedia.sql knownToWikipedia.tab #end didn't do # MAKE FOLDUTR TABLES # First set up directory structure and extract UTR sequence on hgwdev # TODO, doesn't work with tmpFoo1 (nibPath is NULL) tempDb=braNey38 cd $dir mkdir -p rnaStruct cd rnaStruct mkdir -p utr3/split utr5/split utr3/fold utr5/fold # these commands take some significant time utrFa $tempDb knownGene utr3 utr3/utr.fa utrFa $tempDb knownGene utr5 utr5/utr.fa # Split up files and make files that define job. faSplit sequence utr3/utr.fa 10000 utr3/split/s faSplit sequence utr5/utr.fa 10000 utr5/split/s ls -1 utr3/split > utr3/in.lst ls -1 utr5/split > utr5/in.lst cd utr3 cat << _EOF_ > template #LOOP rnaFoldBig split/$(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" # 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 # Make pfam run. Actual cluster run is about 6 hours. #mkdir -p /hive/data/outside/pfam/Pfam27.0 #cd /hive/data/outside/pfam/Pfam27.0 #wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz #gunzip Pfam-A.hmm.gz #set pfamScratch = $scratchDir/pfamBR #ssh $cpuFarm mkdir -p $pfamScratch #ssh $cpuFarm cp /hive/data/outside/pfam/Pfam26.0/Pfam-A.hmm $pfamScratch mkdir -p $dir/pfam cd $dir/pfam rm -rf splitProt mkdir splitProt faSplit sequence $dir/ucscGenes.faa 10000 splitProt/ mkdir -p result ls -1 splitProt > prot.list # /hive/data/outside/pfam/hmmpfam -E 0.1 /hive/data/outside/pfam/current/Pfam_fs \ cat << '_EOF_' > doPfam #!/bin/csh -ef /hive/data/outside/pfam/Pfam27.0/PfamScan/hmmer-3.1b1/src/hmmsearch --domtblout /scratch/tmp/pfam.$2.pf --noali -o /dev/null -E 0.1 /hive/data/outside/pfam/Pfam27.0/Pfam-A.hmm splitProt/$1 mv /scratch/tmp/pfam.$2.pf $3 _EOF_ # << happy emacs chmod +x doPfam cat << '_EOF_' > template #LOOP doPfam $(path1) $(root1) {check out line+ result/$(root1).pf} #ENDLOOP _EOF_ gensub2 prot.list single template jobList ssh $cpuFarm "cd $dir/pfam; para make jobList" ssh $cpuFarm "cd $dir/pfam; para time > run.time" cat run.time # Completed: 9577 of 9577 jobs # CPU time in finished jobs: 1898828s 31647.13m 527.45h 21.98d 0.060 y # IO & Wait Time: 823666s 13727.77m 228.80h 9.53d 0.026 y # Average job time: 284s 4.74m 0.08h 0.00d # Longest finished job: 355s 5.92m 0.10h 0.00d # Submission to last job: 9639s 160.65m 2.68h 0.11d # Make up pfamDesc.tab by converting pfam to a ra file first cat << '_EOF_' > makePfamRa.awk /^NAME/ {print} /^ACC/ {print} /^DESC/ {print; printf("\n");} _EOF_ awk -f makePfamRa.awk /hive/data/outside/pfam/Pfam27.0/Pfam-A.hmm > pfamDesc.ra raToTab -cols=ACC,NAME,DESC pfamDesc.ra stdout | awk -F '\t' '{printf("%s\t%s\t%s\n", gensub(/\.[0-9]+/, "", "g", $1), $2, $3);}' > pfamDesc.tab # Convert output to tab-separated file. cd $dir/pfam catDir result | sed '/^#/d' | awk 'BEGIN {OFS="\t"} {if ($7 < 0.0001) print $1,$18-1,$19,$4,$7}' | sort > ucscPfam.tab cd $dir # Convert output to knownToPfam table awk '{printf("%s\t%s\n", $2, gensub(/\.[0-9]+/, "", "g", $1));}' \ pfam/pfamDesc.tab > sub.tab cut -f 1,4 pfam/ucscPfam.tab | subColumn 2 stdin sub.tab stdout | sort -u > knownToPfam.tab rm -f sub.tab hgLoadSqlTab -notOnServer $tempDb knownToPfam $kent/src/hg/lib/knownTo.sql knownToPfam.tab hgLoadSqlTab -notOnServer $tempDb pfamDesc $kent/src/hg/lib/pfamDesc.sql pfam/pfamDesc.tab #hgsql $tempDb -e "delete k from knownToPfam k, kgXref x where k.name = x.kgID and x.geneSymbol = 'abParts'" cd $dir/pfam genePredToFakePsl hg38 knownGene knownGene.psl cdsOut.tab sort cdsOut.tab | sed 's/\.\./ /' > sortCdsOut.tab sort ucscPfam.tab> sortPfam.tab awk '{print $10, $11}' knownGene.psl > gene.sizes join sortCdsOut.tab sortPfam.tab | awk '{print $1, $2 + 3 * $4, $2 + 3 * $5, $6}' | bedToPsl gene.sizes stdin domainToGene.psl pslMap domainToGene.psl knownGene.psl stdout | sort | uniq | pslToBed stdin domainToGenome.bed hgLoadBed $tempDb ucscGenePfam domainToGenome.bed # Do scop run. Takes about 6 hours mkdir /hive/data/outside/scop/1.75 cd /hive/data/outside/scop/1.75 wget "ftp://license:SlithyToves@supfam.org/models/hmmlib_1.75.gz" gunzip hmmlib_1.75.gz wget "ftp://license:SlithyToves@supfam.org/models/model.tab.gz" gunzip model.tab.gz mkdir -p $dir/scop cd $dir/scop rm -rf result mkdir result ls -1 ../pfam/splitProt > prot.list cat << '_EOF_' > doScop #!/bin/csh -ef /hive/data/outside/pfam/Pfam27.0/PfamScan/hmmer-3.1b1/src/hmmsearch --domtblout /scratch/tmp/scop.$2.pf --noali -o /dev/null -E 0.1 /hive/data/outside/scop/1.75/hmmlib_1.75 ../pfam/splitProt/$1 mv /scratch/tmp/scop.$2.pf $3 _EOF_ # << happy emacs chmod +x doScop cat << '_EOF_' > template #LOOP doScop $(path1) $(root1) {check out line+ result/$(root1).pf} #ENDLOOP _EOF_ # << happy emacs gensub2 prot.list single template jobList ssh $cpuFarm "cd $dir/scop; para make jobList" ssh $cpuFarm "cd $dir/scop; para time > run.time" cat run.time # Completed: 9577 of 9577 jobs # CPU time in finished jobs: 1872212s 31203.54m 520.06h 21.67d 0.059 y # IO & Wait Time: 904637s 15077.28m 251.29h 10.47d 0.029 y # Average job time: 290s 4.83m 0.08h 0.00d # Longest finished job: 664s 11.07m 0.18h 0.01d # Submission to last job: 10541s 175.68m 2.93h 0.12d # Convert scop output to tab-separated files cd $dir catDir scop/result | sed '/^#/d' | awk 'BEGIN {OFS="\t"} {if ($7 <= 0.0001) print $1,$18-1,$19,$4, $7,$8}' | sort > scopPlusScore.tab sort -k 2 /hive/data/outside/scop/1.75/model.tab > scop.model.tab scopCollapse scopPlusScore.tab scop.model.tab ucscScop.tab \ scopDesc.tab knownToSuper.tab hgLoadSqlTab -notOnServer $tempDb scopDesc $kent/src/hg/lib/scopDesc.sql scopDesc.tab hgLoadSqlTab $tempDb knownToSuper $kent/src/hg/lib/knownToSuper.sql knownToSuper.tab #hgsql $tempDb -e "delete k from knownToSuper k, kgXref x where k.gene = x.kgID and x.geneSymbol = 'abParts'" hgLoadSqlTab $tempDb ucscScop $kent/src/hg/lib/ucscScop.sql ucscScop.tab # Regenerate ccdsKgMap table # TODO: didn't do $kent/src/hg/makeDb/genbank/bin/x86_64/mkCcdsGeneMap -db=$tempDb -loadDb $db.ccdsGene knownGene ccdsKgMap # Do BioCyc Pathways build export bioCycDir=/hive/data/outside/bioCyc/140219/download/17.5/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 hg38 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 # Do KEGG Pathways build (borrowing Fan Hus's strategy from hg38.txt) 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.13/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; 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 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}__$2/ || die;' \ > idSub.txt # 2. Get a file of per-transcript fasta sequences that contain the sequences of each UCSC Genes transcript, with this new ID in the place of the UCSC Genes accession. Convert that file to TwoBit format and soft-link it into /gbdb/hg38/targetDb/ subColumn 4 ucscGenes.bed idSub.txt ucscGenesIdSubbed.bed sequenceForBed -keepName -db=$db -bedIn=ucscGenesIdSubbed.bed -fastaOut=stdout | faToTwoBit stdin kgTargetSeq${curVer}.2bit mkdir -p /gbdb/$db/targetDb/ rm -f /gbdb/$db/targetDb/kgTargetSeq${curVer}.2bit ln -s $dir/kgTargetSeq${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 # # At this point we should save a list of the tables in tempDb!!! echo "show tables" | hgsql $tempDb > tablesInKnownGene.lst # got hg38.knownGene.tables.txt from the last push request hgsql $db -e "show tables like 'knownTo%'" | tail -n +2 | sort > hg38.knownTo.txt join -v 1 hg38.knownTo.txt hg38.knownGene.tables.txt #knownToGencodeV20 #knownToGnf1h #knownToGnfAtlas2 #knownToMalacards #knownToU133 #knownToU95 cat hg38.knownTo.txt hg38.knownGene.tables.txt | sort -u > hg38.all.knownGene.tables.txt # added ccdsKgMap gnfAtlas2Distance gnfU95Distance for i in `cat hg38.all.knownGene.tables.txt`; do echo "desc $i;" | hgsql $tempDb; done 2>&1 | grep exist | awk '{print $8}' > missing.tables.txt join -v 1 tablesInKnownGene.lst hg38.all.knownGene.tables.txt # kg8ToKg9 # kgXrefOld8 # knownGeneOld8 # knownToEnsembl # knownToGencodeV22 # knownToMrna # knownToMrnaSingle # knownToTag join -v 2 tablesInKnownGene.lst hg38.all.knownGene.tables.txt #kg7ToKg8 #kgProtMap2 #kgTxInfo #knownGeneTxMrna #knownGeneTxPep #knownToGencodeV20 #knownToGnf1h #knownToWikipedia # Create backup database hgsqladmin create ${db}Backup # Swap in new tables, moving old tables to backup database. for i in `cat hg38.all.knownGene.tables.txt` do echo "rename table $db.$i to ${db}Backup.$i;" | hgsql $db; done for i in `cat tablesInKnownGene.lst` do echo "rename table $tempDb.$i to ${db}.$i;" | hgsql $db done hgsqladmin flush-tables # Make full text index. Takes a minute or so. After this the genome browser # tracks display will work including the position search. The genes details # NOW SWAP IN TABLES FROM TEMP DATABASE TO MAIN DATABASE. # You'll need superuser powers for this step..... cd $dir # Drop tempDb history table and chromInfo, we don't want to swap them in! hgsql -e "drop table history" $tempDb hgsql -e "drop table chromInfo" $tempDb cat << _EOF_ > moveTablesIntoPlace # Save old known genes and kgXref tables sudo ~kent/bin/copyMysqlTable $db knownGene $tempDb knownGeneOld$lastVer sudo ~kent/bin/copyMysqlTable $db kgXref $tempDb kgXrefOld$lastVer # Create backup database hgsqladmin create ${db}BackupBraney2 # Swap in new tables, moving old tables to backup database. sudo ~kent/bin/swapInMysqlTempDb $tempDb $db ${db}BackupBraney2 _EOF_ # Update database links. sudo rm /var/lib/mysql/uniProt sudo ln -s /var/lib/mysql/$spDb /var/lib/mysql/uniProt sudo rm /var/lib/mysql/proteome sudo ln -s /var/lib/mysql/$pbDb /var/lib/mysql/proteome hgsqladmin flush-tables # Make full text index. Takes a minute or so. After this the genome browser # tracks display will work including the position search. The genes details # page, gene sorter, and proteome browser still need more tables. mkdir -p $dir/index cd $dir/index hgKgGetText $db knownGene.text ixIxx knownGene.text knownGene.ix knownGene.ixx rm -f /gbdb/$db/knownGene.ix /gbdb/$db/knownGene.ixx ln -s $dir/index/knownGene.ix /gbdb/$db/knownGene.ix ln -s $dir/index/knownGene.ixx /gbdb/$db/knownGene.ixx # 3. Ask cluster-admin to start an untranslated, -stepSize=5 gfServer on # /gbdb/$db/targetDb/kgTargetSeq${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 hg38KgSeq9 blat4c, port 17869. hgsql hgcentraltest -e \ 'INSERT into blatServers values ("hg38KgSeq9", "blat4c", 17869, 0, 1);' hgsql hgcentraltest -e \ 'INSERT into targetDb values("hg38KgSeq9", "UCSC Genes", \ "hg38", "kgTargetAli", "", "", \ "/gbdb/hg38/targetDb/kgTargetSeq9.2bit", 1, now(), "");' # ## ## WRAP-UP # # add database to the db's in kent/src/hg/visiGene/vgGetText cd $dir # # Finally, need to wait until after testing, but update databases in other organisms # with blastTabs # Load blastTabs cd $dir/hgNearBlastp hgLoadBlastTab $xdb $blastTab run.$xdb.$tempDb/out/*.tab hgLoadBlastTab $ratDb $blastTab run.$ratDb.$tempDb/out/*.tab hgLoadBlastTab $flyDb $blastTab run.$flyDb.$tempDb/recipBest.tab hgLoadBlastTab $wormDb $blastTab run.$wormDb.$tempDb/recipBest.tab hgLoadBlastTab $yeastDb $blastTab run.$yeastDb.$tempDb/recipBest.tab #hgLoadBlastTab $fishDb $blastTab run.$fishDb.$tempDb/recipBest.tab # Do synteny on mouse/human/rat synBlastp.csh $xdb $db # old number of unique query values: 44985 # old number of unique target values 22854 # new number of unique query values: 41649 # new number of unique target values 22340 synBlastp.csh $ratDb $db rgdGene2 knownGene #old number of unique query values: 11216 #old number of unique target values 10819 #new number of unique query values: 8112 #new number of unique target values 8182 # need to generate multiz downloads #/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz46way/alignments/knownCanonical.exonAA.fa.gz #/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz46way/alignments/knownCanonical.exonNuc.fa.gz #/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz46way/alignments/knownGene.exonAA.fa.gz #/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz46way/alignments/knownGene.exonNuc.fa.gz #/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz46way/alignments/md5sum.txt echo echo "see the bottom of the script for details about knownToWikipedia" echo # Clean up rm -r run.*/out # Last step in setting up isPCR: after the new UCSC Genes with the new Known Gene isPcr # is released, take down the old isPcr gfServer ####################### ### The following is the process Briam Lee used to pull out only # the genes from knownToLocusLink for which there are Wikipedia articles. ### get the full knownToLocusLinkTable # hgsql -Ne 'select value from knownToLocusLink' hg38 | sort -u >> knToLocusLink ### query Wikipedia for each to if there is an article # for i in $(cat knToLocusLink); do lynx -dump "http://genewiki.sulab.org/map/wiki/"$i | grep -m 1 "no results" >trash ; echo $? $i | grep "1 "| awk '{print $2}'>> workingLinks; done ### pull out all isoforms that have permitted LocusLinkIds # for i in $(cat workingLinks); do hgsql -Ne 'select * from knownToLocusLink where value like "'$i'"' hg38 >> knownToWikipediaNew; done ### then load the table as knownToWikipedia using the knowToLocusLink INDICES. ## braney's knownToWikipedia logic # maybe rescrape wikipedia following instructions in doc/wikipediaScrape.txt mkdir $dir/wikipedia cd $dir/wikipedia hgsql hg38 -e "select geneSymbol,name from knownGene g, kgXref x where g.name=x.kgId " | sort > hg38.symbolToId.txt join -t $'\t' /hive/groups/browser/wikipediaScrape/symbolToPage.txt hg38.symbolToId.txt | tawk '{print $3,$2}' | sort | uniq > hg38.idToPage.txt hgLoadSqlTab hg38 knownToWikipedia $HOME/kent/src/hg/lib/knownTo.sql hg38.idToPage.txt