Commit bcaea43d authored by Eric Coissac's avatar Eric Coissac

Adds options to allows to disconnect some detectors

parent c27edd09
......@@ -22,6 +22,9 @@ source "${THIS_DIR}/scripts/bash_init.sh"
taxid="no"
normalization="yes"
irdetection="yes"
cdsdetection="yes"
trnadetection="yes"
rrnadetection="yes"
organism="no"
types="chloro"
partial=0
......@@ -71,7 +74,7 @@ function fastaIterator() {
}
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:o:icrmhpl: -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help -- "$@")
if ! options=$(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 -- "$@")
then
# something went wrong, getopt will put out an error message for us
usage $0 1
......@@ -91,6 +94,9 @@ do
-p|--partial) partial="1" ;;
-l|--min-length) minlength="$2" ; shift ;;
-h|--help) usage $0 0;;
-C|--no-cds) cdsdetection="no";;
-T|--no-trna) trnadetection="no";;
-R|--no-rrna) rrnadetection="no";;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
(*) break;;
......@@ -158,17 +164,23 @@ pushTmpDir ORG.organnot
touch "${RESULTS}.annot"
fi
loginfo "Annotating the tRNA..."
if [[ "$trnadetection" == "yes" ]] ; then
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Done."
fi
loginfo "Annotating the rRNA genes..."
if [[ "$rrnadetection" == "yes" ]] ; then
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Done."
fi
loginfo "Annotating the CDS..."
if [[ "$cdsdetection" == "yes" ]] ; then
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.csh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Done."
fi
if (( partial == 0 )) ; then
topology="circular"
......
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