b209ddecd094d68684158d3b22c7ba1a23c06f8c
braney
  Thu Jun 27 12:58:43 2024 -0700
strip off _# at end of id for knownToEnsembl if it's there (like it is on hg19)

diff --git src/hg/utils/otto/knownGene/buildTo.sh src/hg/utils/otto/knownGene/buildTo.sh
index aab8c8c..002d58d 100755
--- src/hg/utils/otto/knownGene/buildTo.sh
+++ src/hg/utils/otto/knownGene/buildTo.sh
@@ -1,124 +1,124 @@
 #!/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 != '' and locusLinkId != ''" $db > refToLl.txt
 hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db ncbiRefSeq knownGene knownToLocusLink -lookup=refToLl.txt
 rm refToLl.txt
 
 if test "$gtexGeneModel" != ""
 then
     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
+awk '{OFS="\t"} {new=$4;gsub("_.*$","",new);print $4,new}' ucscGenes.bed | sort | uniq > knownToEnsembl.tab
 cp knownToEnsembl.tab knownToGencode${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
 
 #rm lynxExists.txt geneSymbolToKgId.txt
 
 # load malacards table
 if test "$malacardTable" != ""
 then
     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
     rm geneSymbolToKgId.txt malacardExists.txt knownToMalacard.txt
 fi
 
 #knownToVisiGene
 knownToVisiGene $tempDb -probesDb=$db
 
 hgsql $tempDb -e "select geneSymbol,name from knownGene g, kgXref x where g.name=x.kgId " | sort > $tempDb.symbolToId.txt
 join -t $'\t'   /hive/groups/browser/wikipediaScrape/symbolToPage.txt $tempDb.symbolToId.txt | tawk '{print $3,$2}' | sort | uniq > $tempDb.idToPage.txt
 hgLoadSqlTab $tempDb knownToWikipedia $HOME/kent/src/hg/lib/knownTo.sql $tempDb.idToPage.txt
 
 
 if test "$gnfU133TableLookup" != ""
 then
     hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db affyU133 knownGene $gnfU133TableLookup
 fi
 
 if test "$gnfAtlasTableLookup" != ""
 then
     hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db gnfAtlas2 knownGene $gnfAtlasTableLookup '-type=bed 12'
 
     if test  "$gnfAtlasTablesFixed" != ""
     then
         time hgExpDistance $tempDb $gnfAtlasTablesFixed gnfAtlas2Distance \
                         -lookup=$gnfAtlasTableLookup
     fi
 fi
 
 if test "$gnfU95TableLookup" != ""
 then
     hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db affyU95 knownGene $gnfU95TableLookup
     if test  "$gnfU95TablesFixed" != ""
     then
         time hgExpDistance $tempDb $gnfU95TablesFixed gnfU95Distance  -lookup=$gnfU95TableLookup
     fi
 fi
 
 if test "$hprd_file" != ""
 then
 # Commented out these fetch lines until the hprd.org website returns.  In the meantime,
 # you can copy the files from the previous build (they haven't changed in a while).
 #    wget "$hprd_website/$hprd_tar"
 #    tar xvf $hprd_tar
     cp ${oldGeneDir}/${hprd_tar} .
     cp -R `dirname ${oldGeneDir}/${hprd_file}` ./`dirname ${hprd_file}`
     knownToHprd $tempDb $hprd_file
     hgLoadNetDist $genomes/hg19/p2p/hprd/hprd.pathLengths $tempDb humanHprdP2P \
         -sqlRemap="select distinct value, name from knownToHprd"
 
     # these should be under a different test, but...
     hgLoadNetDist $genomes/hg19/p2p/vidal/humanVidal.pathLengths $tempDb humanVidalP2P -sqlRemap="select distinct locusLinkID, kgID from hgFixed.refLink,kgXref where hgFixed.refLink.mrnaAcc = kgXref.refSeq"
     hgLoadNetDist $genomes/hg19/p2p/wanker/humanWanker.pathLengths $tempDb humanWankerP2P -sqlRemap="select distinct locusLinkID, kgID from hgFixed.refLink,kgXref where hgFixed.refLink.mrnaAcc = kgXref.refSeq"
 
 fi
 
 # mupit-pdbids.txt was emailed from Kyle Moad (kmoad@insilico.us.com)
 # wc -l 
 cp /hive/data/outside/mupit/mupit-pdbids.txt .
 # get knownGene IDs and associated PDB IDS
 # 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 "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
 
 # 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