030eb76bec5c124428fd35626ea30609df945cbc jcasper Wed Aug 23 15:44:06 2023 -0700 Slight name change to improve readability, no ticket diff --git src/hg/utils/otto/knownGene/buildTo.sh src/hg/utils/otto/knownGene/buildTo.sh index 0edf72a..c163074 100755 --- src/hg/utils/otto/knownGene/buildTo.sh +++ src/hg/utils/otto/knownGene/buildTo.sh @@ -1,29 +1,29 @@ #!/bin/sh -ex { . ./buildEnv.sh # knownToLocusLink #hgsql --skip-column-names -e "select mrnaAcc,locusLinkId from hgFixed.refLink" $db > refToLl.txt hgsql --skip-column-names -e "select mrnaAcc,locusLinkId from ncbiRefSeqLink where mrnaAcc != ''" $db > refToLl.txt hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db ncbiRefSeq knownGene knownToLocusLink -lookup=refToLl.txt rm refToLl.txt -if test "$gtexGeneMode" != "" +if test "$gtexGeneModel" != "" then - hgMapToGene -geneTableType=genePred $db -tempDb=$tempDb -all -type=genePred $gtexGeneMode knownGene knownToGtex + hgMapToGene -geneTableType=genePred $db -tempDb=$tempDb -all -type=genePred $gtexGeneModel knownGene knownToGtex fi # knownToEnsembl and knownToGencode${GENCODE_VERSION} 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 #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 @@ -93,26 +93,28 @@ # the extDb{Ref} parts come from hg/hgGene/domains.c:domainsPrint() hgsql -Ne "select kgID, extAcc1 from $tempDb.kgXref x \ inner join sp180404.extDbRef sp on x.spID = sp.acc \ inner join sp180404.extDb e on sp.extDb=e.id \ where x.spID != '' and e.val='PDB' order by kgID" \ > $tempDb.knownToPdb.txt; # filter out pdbIds not found in mupit cat mupit-pdbids.txt | tr '[a-z]' '[A-Z]' | \ grep -Fwf - $tempDb.knownToPdb.txt > knownToMupit.txt; # check that it filtered correctly: # cut -f2 $db.knownToMuipit.txt | sort -u | wc -l; # load new table for hgGene/hgc hgLoadSqlTab $tempDb knownToMupit ~/kent/src/hg/lib/knownTo.sql knownToMupit.txt # make knownToNextProt -wget "ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt" +#wget "ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt" +wget "https://download.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 $tempDb | 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 $kent/src/hg/lib/knownTo.sql knownToNextProt.tab -hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db HInvGeneMrna knownGene knownToHInv +# H-Inv is no longer built (last on hg19) +#hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db HInvGeneMrna knownGene knownToHInv echo "BuildKnownTo successfully finished" } > doKnownTo.log < /dev/null 2>&1