21ecc89a7989c1f60d6da19c6e9eeb2dbe65525d
braney
  Wed Sep 1 12:07:30 2021 -0700
update to blastTabs to mm39 from mm10

diff --git src/hg/utils/otto/knownGene/buildLoadOther.sh src/hg/utils/otto/knownGene/buildLoadOther.sh
new file mode 100755
index 0000000..e3dafda
--- /dev/null
+++ src/hg/utils/otto/knownGene/buildLoadOther.sh
@@ -0,0 +1,123 @@
+#!/bin/sh -ex
+cd $dir
+
+{
+# 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
+# make sure all the fasta is there
+ls -l $tempFa
+ls -l $xdbFa
+ls -l $ratFa
+ls -l $fishFa
+ls -l $flyFa
+ls -l $wormFa
+ls -l $yeastFa
+
+( cat << ThisEnd
+# 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
+ThisEnd
+) > config.ra
+
+rm -rf  $scratchDir/brHgNearBlastp
+doHgNearBlastp.pl -noLoad -clusterHub=ku -distrHost=hgwdev -dbHost=hgwdev -workhorse=hgwdev config.ra 
+
+# Load self
+cd $dir/hgNearBlastp/run.$tempDb.$tempDb
+# builds knownBlastTab
+./loadPairwise.csh
+
+# Load human and rat
+cd $dir/hgNearBlastp/run.$tempDb.$xdb
+hgLoadBlastTab $tempDb $xBlastTab -maxPer=1 out/*.tab
+cd $dir/hgNearBlastp/run.$tempDb.$ratDb
+hgLoadBlastTab $tempDb $rnBlastTab -maxPer=1 out/*.tab
+
+# Remove non-syntenic hits for human and rat
+# Takes a few minutes
+mkdir -p /gbdb/$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: 62743
+# old number of unique target values 27998
+# new number of unique query values: 54818
+# new number of unique target values 26309
+
+synBlastp.csh $tempDb $ratDb knownGene ensGene
+# old number of unique query values: 63123
+# old number of unique target values 21163
+# new number of unique query values: 57012
+# new number of unique target values 20298
+
+# 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
+
+# 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
+
+# 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
+
+# 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
+
+# Clean up
+cd $dir/hgNearBlastp
+cat run.$tempDb.$tempDb/out/*.tab | gzip -c > run.$tempDb.$tempDb/all.tab.gz
+gzip run.*/all.tab
+
+echo "BuildBlast successfully finished"
+} > doBlast.log 2>&1