Commit e8357a63 by Eric Coissac

Patch a bug to launch exonerate on complexe filename

parent 626566f2
......@@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName
#
# Alias the genome filename to a short name
# to circumvent a bug in exonerate
set ShortLink = $OutDir/genome.fasta
ln -s $GenoFile $ShortLink
echo $GenoFile | grep '^/' > /dev/null
if ( $status == 1 ) then
set AbsGenoFile = `pwd`/$GenoFile
set DirGenoFile = `dirname $AbsGenoFile`
set DirGenoFile = `(cd $DirGenoFile;pwd)`
set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
else
set AbsGenoFile = $GenoFile
endif
set ShortDir = `mktemp -d`
set ShortLink = $ShortDir/genome.fasta
ln -s $AbsGenoFile $ShortLink
Notify " Building input shortcut $AbsGenoFile --> $ShortLink"
#
# skip exonerate calculations if already done
......@@ -232,7 +245,8 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
# end
#
rm -f $ShortLink
rm -rf $ShortDir
Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null
......
......@@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust")
endif
end
cp $temp/ $Genome.cds.fasta $Genome.cds.fasta
#
# pass2: transsplicing
#
......@@ -71,6 +73,8 @@ end
# pass3: prokov
#
$PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
#
# end : output on stdout
#
......
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