Commit 6600123f authored by Eric Coissac's avatar Eric Coissac

Change some blastx parametter to get better matches by taking into

account intron size and the good genetic code
parent 30f2caea
......@@ -12,6 +12,9 @@ unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
set ParamsDir = $PROG_DIR/../params
set ModelsDir = $PROG_DIR/../models
NeedArg 2
set GenoFile = $Argv[1]; Shift
......@@ -19,6 +22,14 @@ set ProtFile = $Argv[1]; Shift
NeedFile $GenoFile
NeedFile $ProtFile
NeedFile $ParamsDir/default
#
# general parameters
#
source $ParamsDir/default
set IDMIN = 70
set NBMIN = 50
......@@ -43,7 +54,9 @@ endif
#
Notify " blasting $ProtFile"
blastx -query $GenoFile -db $ProtFile -outfmt 7 |\
blastx -query $GenoFile -db $ProtFile -outfmt 7 \
-query_gencode $PASS1_BLASTX_FILTER_GCODE \
-max_intron_length $PASS1_MAX_INTRON |\
$AwkCmd -v IDMIN=$IDMIN \
-v NBMIN=$NBMIN \
-v NBMAX=$NBMAX \
......
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