Commit 0a5ece1e by Eric Coissac

Always a new attempt to solve the bug...

parent ca048f8c
......@@ -108,25 +108,6 @@ endif
set base = $OutDir/$GenoName.$ProtName
#
# Alias the genome filename to a short name
# to circumvent a bug in exonerate
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 --> $ShortLink"
#
# skip exonerate calculations if already done
#
......@@ -141,7 +122,7 @@ endif
if ($PASS1_SPEEDUP != 0) then
tcsh -f $PROG_DIR/do_filterbx.csh $ShortLink $ProtFile \
tcsh -f $PROG_DIR/do_filterbx.csh $GenoFile $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$
......@@ -187,7 +168,7 @@ exonerate \
--refineboundary 5000 \
--singlepass FALSE \
--dpmemory 1024 \
$DbFile $ShortLink > $base.exo.raw
$DbFile $GenoFile > $base.exo.raw
CheckAbort 20 "exonerate failure"
#
......@@ -211,7 +192,7 @@ egrep "^$ProtName " $ProtDir/Annot.lst | $AwkCmd '{print "c annot", $0}' > T_$$
#
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
-v FASTA=$ShortLink \
-v FASTA=$GenoFile \
-v START_MODEL=$STARTMODEL \
-v STOP_MODEL=$STOPMODEL \
-v START_WALK=$PASS1_START_WALK \
......@@ -223,14 +204,14 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
echo "c pass pass1 $ProtType" > $base.iff
$AwkCmd -v FASTA=$ShortLink -f $LIB_DIR/libutil.awk \
$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/translate.awk T_$$ >> $base.iff
#
# extract CDS
#
$AwkCmd -v FASTA=$ShortLink -f $LIB_DIR/libutil.awk \
$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/cds.awk T_$$ >> $OutDir/$GenoName.cds.fasta
......@@ -245,8 +226,6 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
# end
#
rm -rf $ShortDir
Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null
......
......@@ -43,13 +43,33 @@ NeedDir $DbRoot/models
# run everything into temporary place
#
set temp = $Genome.tmp
set temp = `hostname`.$$.Genome.tmp
if (! -d $temp) then
Notify "making directory $temp"
mkdir $temp
endif
#
# find the absolute path of the fasta genome file
#
echo $Fasta | grep '^/' > /dev/null
if ( $status == 1 ) then
set AbsGenoFile = `pwd`/$Fasta
set DirGenoFile = `dirname $AbsGenoFile`
set DirGenoFile = `(cd $DirGenoFile;pwd)`
set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
else
set AbsGenoFile = $Fasta
endif
pushd $temp
ln -s $AbsGenoFile genome.fasta
popd
set Fasta = $temp/genome.fasta
#
# pass1: run exonerate
#
......@@ -63,7 +83,7 @@ foreach dir ("core" "shell" "dust")
endif
end
cp $temp/ $Genome.cds.fasta $Genome.cds.fasta
cp $temp/$Genome.cds.fasta $Genome.cds.fasta
#
# pass2: transsplicing
......
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