...
 
Commits (4)
......@@ -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
#
......
......@@ -181,6 +181,10 @@ function Unk(s) {
QQualifier("product", Product)
QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
if (match(Translat,/\*/)>0) {
QQualifier("pseudogene","unknown")
QQualifier("note","nonfunctional due to stop codon")
}
if (FrameShift==0)
QQualifier("translation", Translat)
......
......@@ -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
......