Commit 6600123f by 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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