#!/usr/bin/env tclsh
set argVars {targetDb queryFa outPsl}
set usage "doBlast $argVars"

if {$argc != [llength $argVars]} {
    error "wrong # args: $usage"
}
set blastAll /cluster/bin/blast/x86_64/blast-2.2.16/bin/blastall

foreach var $argVars val $argv {
    set $var $val
}

file mkdir [file dirname $outPsl]
set outPslTmp $outPsl.[exec hostname].[pid]

exec $blastAll -p tblastn -F F -d $targetDb -i $queryFa 2>@stderr | blastToPsl stdin $outPslTmp 2>@stderr
file rename -force $outPslTmp $outPsl
