Commit 318327af authored by Eric Coissac's avatar Eric Coissac

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
parent 11b612fc
...@@ -151,7 +151,8 @@ endif ...@@ -151,7 +151,8 @@ endif
Notify " running exonerate of $GenoName on $ProtName" Notify " running exonerate of $GenoName on $ProtName"
exonerate \ exonerate \
--model protein2genome \ --model protein2genome \
# -E -S no \
--percent $PASS1_PERCENT \ --percent $PASS1_PERCENT \
--showalignment TRUE \ --showalignment TRUE \
--showvulgar TRUE \ --showvulgar TRUE \
...@@ -168,6 +169,7 @@ exonerate \ ...@@ -168,6 +169,7 @@ exonerate \
--refineboundary 5000 \ --refineboundary 5000 \
--singlepass FALSE \ --singlepass FALSE \
--dpmemory 1024 \ --dpmemory 1024 \
--ryo "@@INFO@@ %et %ps" \
$DbFile $GenoFile > $base.exo.raw $DbFile $GenoFile > $base.exo.raw
CheckAbort 20 "exonerate failure" CheckAbort 20 "exonerate failure"
...@@ -181,6 +183,15 @@ $AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN \ ...@@ -181,6 +183,15 @@ $AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN \
-v EXCLUDE=$GenoName \ -v EXCLUDE=$GenoName \
-f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best -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 # get annotations
# #
......
...@@ -44,7 +44,8 @@ AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat ...@@ -44,7 +44,8 @@ AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
# pass1: cluster selection parameters # pass1: cluster selection parameters
# #
AssignUndef PASS1_MAX_SPAN 10000 AssignUndef PASS1_MAX_SPAN 10000
AssignUndef PASS1_ALLOW_STOP 1 AssignUndef PASS1_ALLOW_STOP 0
AssignUndef PASS1_LOOK_FOR_PSEUDO 1
# #
# extension parameters # extension parameters
......
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