Commit a9da8eab authored by Eric Coissac's avatar Eric Coissac

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

too long or complex
parent ba55f354
...@@ -107,6 +107,12 @@ endif ...@@ -107,6 +107,12 @@ endif
set base = $OutDir/$GenoName.$ProtName 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 $ShortLink
# #
# skip exonerate calculations if already done # skip exonerate calculations if already done
# #
...@@ -122,7 +128,7 @@ endif ...@@ -122,7 +128,7 @@ endif
if ($PASS1_SPEEDUP != 0) then 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_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \ $PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$ $PASS1_BLASTX_FILTER_NBMAX > D_$$
...@@ -168,7 +174,7 @@ exonerate \ ...@@ -168,7 +174,7 @@ exonerate \
--refineboundary 5000 \ --refineboundary 5000 \
--singlepass FALSE \ --singlepass FALSE \
--dpmemory 1024 \ --dpmemory 1024 \
$DbFile $GenoFile > $base.exo.raw $DbFile $ShortLink > $base.exo.raw
CheckAbort 20 "exonerate failure" CheckAbort 20 "exonerate failure"
# #
...@@ -192,7 +198,7 @@ egrep "^$ProtName " $ProtDir/Annot.lst | $AwkCmd '{print "c annot", $0}' > T_$$ ...@@ -192,7 +198,7 @@ egrep "^$ProtName " $ProtDir/Annot.lst | $AwkCmd '{print "c annot", $0}' > T_$$
# #
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
-v FASTA=$GenoFile \ -v FASTA=$ShortLink \
-v START_MODEL=$STARTMODEL \ -v START_MODEL=$STARTMODEL \
-v STOP_MODEL=$STOPMODEL \ -v STOP_MODEL=$STOPMODEL \
-v START_WALK=$PASS1_START_WALK \ -v START_WALK=$PASS1_START_WALK \
...@@ -204,8 +210,16 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \ ...@@ -204,8 +210,16 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
echo "c pass pass1 $ProtType" > $base.iff 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_$$ >> $base.iff -f $LIB_DIR/translate.awk T_$$ >> $base.iff
#
# extract CDS
#
$AwkCmd -v FASTA=$ShortLink -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/cds.awk T_$$ >> $OutDir/$GenoName.cds.fasta
# #
# convert to embl # convert to embl
...@@ -218,6 +232,7 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\ ...@@ -218,6 +232,7 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
# end # end
# #
rm -f $ShortLink
Notify " output file: $base.res" Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null (\rm -f ?_$$) >> /dev/null
......
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