dbf1f3970c63ee81e66dca929395aa575a536a26 hiram Thu Apr 30 11:52:20 2026 -0700 eliminate duplicate code section and protect all net tracks with file exist test refs #31811 diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh index db3913da0c3..0b32546f4f9 100755 --- src/hg/utils/automation/asmHubChainNetTrackDb.sh +++ src/hg/utils/automation/asmHubChainNetTrackDb.sh @@ -105,65 +105,49 @@ 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}.$otherDb.liftOverNet.summary.bb fi else printf "# there is NO chainLiftOver${OtherDb}.bb\n" 1>&2 fi if [ -s "$buildDir/trackData/$lastzDir/axtChain/${accessionId}.${otherDb}.quick.bb" ]; then printf "# making quickLift/${otherDb}.bb\n" 1>&2 ln -s ../trackData/$lastzDir/axtChain/${accessionId}.${otherDb}.quick.bb $buildDir/quickLift/${otherDb}.bb ln -s ../trackData/$lastzDir/axtChain/${accessionId}.${otherDb}.quickLink.bb $buildDir/quickLift/${otherDb}.link.bb else printf "# there is NO chainQuickLift${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 @@ -242,49 +226,60 @@ 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 " $((chainNetPriority++)) fi +if [ -s "$buildDir/bbi/${asmId}.$otherDb.net.bb" ] \ + || [ -s "$buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb" ] \ + || [ -s "$buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb" ] \ + || [ -s "$buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb" ]; then + printf " track mafNet${OtherDb}Viewnet shortLabel Net view net visibility full parent chainNet$OtherDb - track net$OtherDb +" + +if [ -s "$buildDir/bbi/${asmId}.$otherDb.net.bb" ]; then + +printf " track net$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 " $((chainNetPriority++)) +fi + if [ -s "$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 " $((chainNetPriority++)) @@ -312,16 +307,18 @@ printf " track liftOverNet$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 +fi # any of the net files exists + done