Commit a9da8eab by Eric Coissac

Patch a bug blocking the exonerate execution when the genome filename is

too long or complex
parent ba55f354
......@@ -108,6 +108,12 @@ endif
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 $ShortLink
#
# skip exonerate calculations if already done
#
......@@ -122,7 +128,7 @@ endif
if ($PASS1_SPEEDUP != 0) then
tcsh -f $PROG_DIR/do_filterbx.csh $GenoFile $ProtFile \
tcsh -f $PROG_DIR/do_filterbx.csh $ShortLink $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$
......@@ -168,7 +174,7 @@ exonerate \
--refineboundary 5000 \
--singlepass FALSE \
--dpmemory 1024 \
$DbFile $GenoFile > $base.exo.raw
$DbFile $ShortLink > $base.exo.raw
CheckAbort 20 "exonerate failure"
#
......@@ -192,7 +198,7 @@ egrep "^$ProtName " $ProtDir/Annot.lst | $AwkCmd '{print "c annot", $0}' > T_$$
#
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
-v FASTA=$GenoFile \
-v FASTA=$ShortLink \
-v START_MODEL=$STARTMODEL \
-v STOP_MODEL=$STOPMODEL \
-v START_WALK=$PASS1_START_WALK \
......@@ -204,8 +210,16 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
echo "c pass pass1 $ProtType" > $base.iff
$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
$AwkCmd -v FASTA=$ShortLink -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/translate.awk T_$$ >> $base.iff
#
# extract CDS
#
$AwkCmd -v FASTA=$ShortLink -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/cds.awk T_$$ >> $OutDir/$GenoName.cds.fasta
#
# convert to embl
......@@ -218,6 +232,7 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
# end
#
rm -f $ShortLink
Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null
......
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