From 2ff6ff33084eb3a1fdbea768e66d3143e0d41335 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 20 Nov 2018 16:02:23 +0100
Subject: [PATCH] If proteins are looked for without stop adds an extra option
 PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
 (Pseudogene search).

The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1

Former-commit-id: 318327af6bdc3fbdfbe7f438ff7cbea22863a0ab
Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
---
 detectors/cds/bin/do_exonerate.csh | 13 ++++++++++++-
 detectors/cds/params/default       |  3 ++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/detectors/cds/bin/do_exonerate.csh b/detectors/cds/bin/do_exonerate.csh
index dfa46fa..03f97fe 100755
--- a/detectors/cds/bin/do_exonerate.csh
+++ b/detectors/cds/bin/do_exonerate.csh
@@ -151,7 +151,8 @@ endif
 
 Notify "  running exonerate of $GenoName on $ProtName"
 exonerate \
-	--model protein2genome            \
+    --model protein2genome            \
+#    -E -S no                         \
     --percent $PASS1_PERCENT          \
     --showalignment TRUE              \
     --showvulgar TRUE                 \
@@ -168,6 +169,7 @@ exonerate \
     --refineboundary 5000             \
     --singlepass FALSE                \
     --dpmemory 1024                   \
+    --ryo "@@INFO@@ %et %ps" \
     $DbFile $GenoFile > $base.exo.raw
 CheckAbort 20 "exonerate failure"
 
@@ -181,6 +183,15 @@ $AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN         \
         -v EXCLUDE=$GenoName                \
         -f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best
 
+if ( -z $base.exo.best) then
+	if ( $PASS1_ALLOW_STOP == "0" && $PASS1_LOOK_FOR_PSEUDO == "1" ) then
+		$AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN         \
+		        -v ALLOW_STOP=1     \
+		        -v EXCLUDE=$GenoName                \
+		        -f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best		
+	endif
+endif
+
 #
 # get annotations
 #
diff --git a/detectors/cds/params/default b/detectors/cds/params/default
index cffece6..aff6734 100644
--- a/detectors/cds/params/default
+++ b/detectors/cds/params/default
@@ -44,7 +44,8 @@ AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
 # pass1: cluster selection parameters
 #
 AssignUndef PASS1_MAX_SPAN    10000
-AssignUndef PASS1_ALLOW_STOP  1
+AssignUndef PASS1_ALLOW_STOP  0
+AssignUndef PASS1_LOOK_FOR_PSEUDO 1
 
 #
 # extension parameters