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cds go_test bug fixed

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Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae
Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
This commit is contained in:
alain viari
2015-11-13 22:37:22 +01:00
parent 42707c281c
commit 405631f527
38 changed files with 231 additions and 37 deletions
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26
detectors/cds/bin/go_cds.sh
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@ -13,7 +13,7 @@
# Results are printed to the standard output
#
#========================================================================================
# usage: go_cds.sh fasta [db_core]
# usage: go_cds.sh fasta [db_root]
#
unsetenv ORG_SOURCED
@ -28,13 +28,16 @@ NeedFile $Fasta
set Genome = `basename $Fasta:r`
set DbCore = $CDS_DATA_DIR/chlorodb/core
set DbRoot = $CDS_DATA_DIR/chlorodb
if ($#Argv > 0) then
set DbCore = $Argv[1]; Shift
set DbRoot = $Argv[1]; Shift
endif
NeedFile $DbCore/Annot.lst
NeedDir $DbRoot/core
NeedFile $DbRoot/core/Annot.lst
NeedDir $DbRoot/models
#
# run everything into temporary place
@ -50,15 +53,16 @@ endif
# pass1: run exonerate
#
set fams = `ls $DbCore/*.fst`
Notify "running pass1: exonerate of $Genome on $DbCore"
foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $temp
foreach dir ("core" "shell" "dust")
if (-d $DbRoot/$dir) then
set fams = `ls $DbRoot/$dir/*.fst`
Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
end
endif
end
#
# pass2: transsplicing
#