#!/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

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