Commit 0ac744e9 authored by Eric Coissac's avatar Eric Coissac

Solve #18

parent f84fd562
......@@ -21,9 +21,10 @@ source "${THIS_DIR}/scripts/bash_init.sh"
taxid="no"
normalization="yes"
irdetection="yes"
organism="no"
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:ih -l ncbi-taxid:,no-ir-detection,help -- "$@")
if ! options=$(getopt -o t:o:ih -l ncbi-taxid:,organism,no-ir-detection,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
exit 1
......@@ -36,6 +37,7 @@ do
case $1 in
-t|--ncbi-taxid) taxid="$2" ; shift;;
-i|--no-ir-detection) irdetection="no" ;;
-o|--organism) organism="$2" ; shift;;
-h|--help) echo "Usage:" ;
echo " $0 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
echo " [-i|--no-ir-detection] [-h|--help] <FASTAFILE>"
......@@ -96,8 +98,20 @@ pushTmpDir ORG.organnot
${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..."
loginfo "Printing minimal header..."
echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "XX"
echo "AC XXX;"
echo "XX"
if [[ "${organism}" == "no" ]]; then
echo "DE {organism} plastid, complete genome."
else
echo "DE $(echo ${organism} | tr '_' ' ') plastid, complete genome."
fi
echo "XX"
loginfo "Done."
loginfo "Printing annotations header..."
echo "FH Key Location/Qualifiers"
loginfo "Done."
......
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