From f74bb0d9738180eb287a5d738752342c8d7c9535 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 23 Jan 2018 07:32:12 +0100
Subject: [PATCH] Patch a bug blocking the exonerate execution when the genome
 filename is too long or complex

Former-commit-id: a9da8eab920f422609b41be2e16d65e0569f953c
Former-commit-id: 6829ae3081bea4a1d16ec8d3bad10e51f01f51d7
---
 detectors/cds/bin/do_exonerate.csh | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/detectors/cds/bin/do_exonerate.csh b/detectors/cds/bin/do_exonerate.csh
index 7a20987..316299e 100755
--- a/detectors/cds/bin/do_exonerate.csh
+++ b/detectors/cds/bin/do_exonerate.csh
@@ -107,6 +107,12 @@ 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