21f4b0da7fe6f8d64ba6d67cabb4bb464df44112 hiram Tue Jan 31 12:21:53 2023 -0800 correct symlink to ../trackData/ not to ../trackDb/ no redmine diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh index 9dcc899..2bc48fc 100755 --- src/hg/utils/automation/asmHubChainNetTrackDb.sh +++ src/hg/utils/automation/asmHubChainNetTrackDb.sh @@ -1,313 +1,313 @@ #!/bin/bash set -beEu -o pipefail set -x if [ $# -ne 2 ]; then printf "usage: asmHubChainNetTrackDb.pl <asmId> <pathTo/assembly hub build directory> > chainNettrackDb.txt\n" 1>&2 printf "expecting to find *.ucsc.2bit and bbi/ files at given path\n" 1>&2 printf "the ncbi|ucsc selects the naming scheme\n" 1>&2 exit 255 fi export asmId=$1 export buildDir=$2 export hubLinks="/hive/data/genomes/asmHubs/hubLinks" export accessionId="${asmId}" case ${asmId} in GC*) accessionId=`echo "$asmId" | awk -F"_" '{printf "%s_%s", $1, $2}'` ;; esac export scriptDir="$HOME/kent/src/hg/utils/automation" mkdir -p $buildDir/bbi mkdir -p $buildDir/liftOver export chainNetPriority=1 printf "# asmHubChainNetTrackDb.pl $asmId $buildDir\n" 1>&2 for D in ${buildDir}/trackData/lastz.* do targetDb=$accessionId lastzDir=`basename "${D}"` otherDb=`echo $lastzDir | sed -e 's/lastz.//;'` OtherDb="${otherDb^}" asmReport=`ls -d $buildDir/download/*assembly_report.txt 2> /dev/null` overChain="${targetDb}.${otherDb}.over.chain.gz" overToChain="${targetDb}To${OtherDb}.over.chain.gz" printf "asmReport: %s\n" "${asmReport}" 1>&2 if [ ! -s "${asmReport}" ]; then printf "# ERROR: can not find assembly_report.txt in $buildDir/download\n" 1>&2 exit 255 fi if [ ! -s ${buildDir}/trackData/$lastzDir/axtChain/chain${OtherDb}.bb ]; then printf "# ERROR: can not find chain${OtherDb}.bb in $buildDir/trackData/$lastzDir/axtChain/\n" 1>&2 exit 255 fi rm -f $buildDir/bbi/${asmId}.chain$OtherDb.bb rm -f $buildDir/bbi/${asmId}.chain${OtherDb}Link.bb rm -f $buildDir/bbi/${asmId}.chainSyn$OtherDb.bb rm -f $buildDir/bbi/${asmId}.chainSyn${OtherDb}Link.bb rm -f $buildDir/bbi/${asmId}.chainRBest$OtherDb.bb rm -f $buildDir/bbi/${asmId}.chainRBest${OtherDb}Link.bb rm -f $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb rm -f $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb rm -f $buildDir/bbi/${asmId}.$otherDb.net.bb rm -f $buildDir/bbi/${asmId}.$otherDb.net.summary.bb rm -f $buildDir/bbi/${asmId}.$otherDb.synNet.bb rm -f $buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb rm -f $buildDir/bbi/${asmId}.$otherDb.rbestNet.bb rm -f $buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb rm -f $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb rm -f $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb rm -f $buildDir/liftOver/${overToChain} if [ -s "$buildDir/trackData/$lastzDir/axtChain/${overChain}" ]; then - ln -s ../trackDb/$lastzDir/axtChain/${overChain} $buildDir/liftOver/${overToChain} + ln -s ../trackData/$lastzDir/axtChain/${overChain} $buildDir/liftOver/${overToChain} fi if [ -s "$buildDir/trackData/$lastzDir/axtChain/chain${OtherDb}.bb" ]; then ln -s ../trackData/$lastzDir/axtChain/chain${OtherDb}.bb $buildDir/bbi/${asmId}.chain$OtherDb.bb ln -s ../trackData/$lastzDir/axtChain/chain${OtherDb}Link.bb $buildDir/bbi/${asmId}.chain${OtherDb}Link.bb fi if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.bb" ]; then ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.bb $buildDir/bbi/${asmId}.$otherDb.net.bb ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.summary.bb $buildDir/bbi/${asmId}.$otherDb.net.summary.bb fi if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainSyn${OtherDb}.bb" ]; then ln -s ../trackData/$lastzDir/axtChain/chainSyn${OtherDb}.bb $buildDir/bbi/${asmId}.chainSyn$OtherDb.bb ln -s ../trackData/$lastzDir/axtChain/chainSyn${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainSyn${OtherDb}Link.bb fi if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb" ]; then ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb $buildDir/bbi/${asmId}.$otherDb.synNet.bb ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb fi if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb" ]; then ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb $buildDir/bbi/${asmId}.chainRBest$OtherDb.bb ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainRBest${OtherDb}Link.bb fi if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb" ]; then ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.bb ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb fi if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb" ]; then printf "# making chainLiftOver${OtherDb}.bb\n" 1>&2 ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb else printf "# there is NO chainLiftOver${OtherDb}.bb\n" 1>&2 fi otherPrefix=`echo $otherDb | cut -c1-2` if [ "${otherPrefix}" = "GC" ]; then sciName=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *//i; s/ *(.*//;'` organism=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *.*(//i; s/).*//;'` taxId=`grep -i 'taxid:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*taxid: *//i;'` o_date=`grep -i 'date:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*date: *//i;'` matrix="" linGap="" minScore="" else organism=`hgsql -N -e "select organism from dbDb where name=\"$otherDb\"" hgcentraltest` sciName=`hgsql -N -e "select scientificName from dbDb where name=\"$otherDb\"" hgcentraltest` taxId=`hgsql -N -e "select taxId from dbDb where name=\"$otherDb\"" hgcentraltest` o_date=`hgsql -N -e "select description from dbDb where name=\"$otherDb\"" hgcentraltest` matrix=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep matrix` fi otherPrefix=`echo $otherDb | cut -c1-2` if [ "${otherPrefix}" = "GC" ]; then sciName=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *//i; s/ *(.*//;'` organism=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *.*(//i; s/).*//;'` taxId=`grep -i 'taxid:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*taxid: *//i;'` o_date=`grep -i 'date:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*date: *//i;'` matrix="" linGap="" minScore="" else organism=`hgsql -N -e "select organism from dbDb where name=\"$otherDb\"" hgcentraltest` sciName=`hgsql -N -e "select scientificName from dbDb where name=\"$otherDb\"" hgcentraltest` taxId=`hgsql -N -e "select taxId from dbDb where name=\"$otherDb\"" hgcentraltest` o_date=`hgsql -N -e "select description from dbDb where name=\"$otherDb\"" hgcentraltest` matrix=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep matrix` minScore=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep MinScore` linGap=`~/kent/src/hg/utils/phyloTrees/findScores.pl $otherDb $targetDb 2>&1 | grep LinearGap` fi printf "############################################################################## # $otherDb - $organism - $sciName - taxId: $taxId ############################################################################## " printf "track chainNet$OtherDb compositeTrack on shortLabel $organism Chain/Net longLabel $organism ($o_date), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno " printf "priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ " if [ "x${matrix}y" = "xy" ]; then printf "otherDb $otherDb html html/$asmId.chainNet " else printf "$matrix $minScore $linGap matrixHeader A, C, G, T otherDb $otherDb html html/$asmId.chainNet " fi printf " track chainNet${OtherDb}Viewchain shortLabel Chain view chain visibility pack parent chainNet$OtherDb spectrum on track chain$OtherDb parent chainNet${OtherDb}Viewchain subGroups view=chain shortLabel $organism Chain longLabel $organism ($o_date) Chained Alignments type bigChain $otherDb bigDataUrl bbi/$asmId.chain$OtherDb.bb linkDataUrl bbi/$asmId.chain${OtherDb}Link.bb priority %d " $((chainNetPriority++)) if [ -s "$buildDir/bbi/${asmId}.chainSyn$OtherDb.bb" ]; then printf " track chainSyn$OtherDb parent chainNet${OtherDb}Viewchain subGroups view=chain shortLabel $organism synChain longLabel $organism ($o_date) Syntenic Chained Alignments type bigChain $otherDb bigDataUrl bbi/$asmId.chainSyn$OtherDb.bb linkDataUrl bbi/$asmId.chainSyn${OtherDb}Link.bb priority %d " $((chainNetPriority++)) fi if [ -s "$buildDir/bbi/${asmId}.chainRBest$OtherDb.bb" ]; then printf " track chainRBest$OtherDb parent chainNet${OtherDb}Viewchain subGroups view=chain shortLabel $organism rbChain longLabel $organism ($o_date) Reciprocal Best Chained Alignments type bigChain $otherDb bigDataUrl bbi/$asmId.chainRBest$OtherDb.bb linkDataUrl bbi/$asmId.chainRBest${OtherDb}Link.bb priority %d " $((chainNetPriority++)) fi if [ -s "$buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb" ]; then printf " track chainLiftOver$OtherDb parent chainNet${OtherDb}Viewchain subGroups view=chain shortLabel $organism loChain longLabel $organism ($o_date) Lift Over Chained Alignments type bigChain $otherDb bigDataUrl bbi/$asmId.chainLiftOver$OtherDb.bb linkDataUrl bbi/$asmId.chainLiftOver${OtherDb}Link.bb priority %d " $((chainNetPriority++)) fi printf " track mafNet${OtherDb}Viewnet shortLabel Net view net visibility full parent chainNet$OtherDb track net$OtherDb parent mafNet${OtherDb}Viewnet subGroups view=net shortLabel $organism net longLabel $organism ($o_date) Net Alignment type bigMaf bigDataUrl bbi/$asmId.$otherDb.net.bb summary bbi/$asmId.$otherDb.net.summary.bb speciesOrder $otherDb priority %d " $((chainNetPriority++)) if [ -s "$buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb" ]; then printf " track synNet$OtherDb parent mafNet${OtherDb}Viewnet subGroups view=net shortLabel $organism synNet longLabel $organism ($o_date) Syntenic Net Alignment type bigMaf bigDataUrl bbi/$asmId.$otherDb.synNet.bb summary bbi/$asmId.$otherDb.synNet.summary.bb speciesOrder $otherDb priority %d " $((chainNetPriority++)) fi if [ -s "$buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb" ]; then printf " track rbestNet$OtherDb parent mafNet${OtherDb}Viewnet subGroups view=net shortLabel $organism rbestNet longLabel $organism ($o_date) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/$asmId.$otherDb.rbestNet.bb summary bbi/$asmId.$otherDb.rbestNet.summary.bb speciesOrder $otherDb priority %d " $((chainNetPriority++)) fi if [ -s "$buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb" ]; then printf " track liftOverNet$OtherDb parent mafNet${OtherDb}Viewnet subGroups view=net shortLabel $organism liftOverNet longLabel $organism ($o_date) Lift Over Net Alignment type bigMaf bigDataUrl bbi/$asmId.$otherDb.liftOverNet.bb summary bbi/$asmId.$otherDb.liftOverNet.summary.bb speciesOrder $otherDb priority %d " $((chainNetPriority++)) fi done