Commit 2489ee1f authored by Eric Coissac's avatar Eric Coissac

Adds new options and call the new bash version of go_cds

parent 36041f96
......@@ -23,6 +23,8 @@ taxid="no"
normalization="yes"
irdetection="yes"
cdsdetection="yes"
cdsdetection_pass1="yes"
cdsdetection_pass2="yes"
trnadetection="yes"
rrnadetection="yes"
organism="no"
......@@ -63,6 +65,21 @@ function usage {
echo
echo ' -l | --min-length'
echo ' Indicates for partial mode the minimum length of contig to annotate'
echo
echo ' -C | --no-cds'
echo ' Do not annotate CDS'
echo
echo ' -D | --no-cds-pass1'
echo ' Do not annotate core CDS'
echo
echo ' -E | --no-cds-pass2'
echo ' Do not annotate rps12 CDS'
echo
echo ' -T | --no-trna'
echo ' Do not look for transfert RNA'
echo
echo ' -R | --no-rrna'
echo ' Do not look for ribosomal RNA'
exit $2
}
......@@ -74,7 +91,7 @@ function fastaIterator() {
}
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:o:icrmhpl:CTR -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help,no-cds,no-trna,no-rrna -- "$@")
if ! options=$(getopt -o t:o:icrmhpl:CDETR -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help,no-cds,no-cds-pass1,no-cds-pass2,no-trna,no-rrna -- "$@")
then
# something went wrong, getopt will put out an error message for us
usage $0 1
......@@ -95,6 +112,8 @@ do
-l|--min-length) minlength="$2" ; shift ;;
-h|--help) usage $0 0;;
-C|--no-cds) cdsdetection="no";;
-D|--no-cds-pass1) cdsdetection_pass1="no";;
-E|--no-cds-pass2) cdsdetection_pass2="no";;
-T|--no-trna) trnadetection="no";;
-R|--no-rrna) rrnadetection="no";;
(--) shift; break;;
......@@ -106,6 +125,11 @@ done
loginfo "Annotating mode.....: $types"
loginfo "IR detection mode...: $irdetection"
loginfo "CDS detection mode..: $cdsdetection"
loginfo " pass 1...: $cdsdetection_pass1"
loginfo " pass 2...: $cdsdetection_pass2"
loginfo "tRNA detection mode.: $trnadetection"
loginfo "rRNA detection mode.: $rrnadetection"
loginfo "Organism............: $organism"
loginfo "Partial mode........: $partial"
loginfo "Minimum length......: $minlength"
......@@ -178,7 +202,9 @@ pushTmpDir ORG.organnot
if [[ "$cdsdetection" == "yes" ]] ; then
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.csh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
cdsdetection_pass1=$cdsdetection_pass1 \
cdsdetection_pass2=$cdsdetection_pass2 \
${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
fi
......
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