PhyloSkims/annotate
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Adds options to allows to disconnect some detectors

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Former-commit-id: bcaea43df50e65508d23bacd9713f4ae02df6ac4
Former-commit-id: d968b9af53164c3dc40483f5b643ffa9390068d0
This commit is contained in:
Eric Coissac
2021-06-01 09:54:04 +02:00
parent 40feaadd43
commit 8e6449bec6
1 changed files with 19 additions and 7 deletions
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26
org-annotate.sh
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@ -22,6 +22,9 @@ source "${THIS_DIR}/scripts/bash_init.sh"
taxid="no" taxid="no"
normalization="yes" normalization="yes"
irdetection="yes" irdetection="yes"
cdsdetection="yes"
trnadetection="yes"
rrnadetection="yes"
organism="no" organism="no"
types="chloro" types="chloro"
partial=0 partial=0
@ -71,7 +74,7 @@ function fastaIterator() {
} }
# options may be followed by one colon to indicate they have a required argument # options may be followed by one colon to indicate they have a required argument
if ! options=$(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 then
# something went wrong, getopt will put out an error message for us # something went wrong, getopt will put out an error message for us
usage $0 1 usage $0 1
@ -91,6 +94,9 @@ do
-p|--partial) partial="1" ;; -p|--partial) partial="1" ;;
-l|--min-length) minlength="$2" ; shift ;; -l|--min-length) minlength="$2" ; shift ;;
-h|--help) usage $0 0;; -h|--help) usage $0 0;;
-C|--no-cds) cdsdetection="no";;
-T|--no-trna) trnadetection="no";;
-R|--no-rrna) rrnadetection="no";;
(--) shift; break;; (--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;; (-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
(*) break;; (*) break;;
@ -158,17 +164,23 @@ pushTmpDir ORG.organnot
touch "${RESULTS}.annot" touch "${RESULTS}.annot"
fi fi
loginfo "Annotating the tRNA..." if [[ "$trnadetection" == "yes" ]] ; then
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot" ${PROG_DIR}/detectors/trna/bin/go_trna.sh "${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" ${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${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" tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.csh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done." loginfo "Done."
fi
if (( partial == 0 )) ; then if (( partial == 0 )) ; then
topology="circular" topology="circular"