Commit bba6581b authored by Eric Coissac's avatar Eric Coissac

remove the printing of an extra empty line at the beginning of the embl

file
parent ee54019d
......@@ -60,7 +60,7 @@ function usage {
if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
exit 1
usage $0 1
fi
eval set -- "$options"
......@@ -82,11 +82,11 @@ do
shift
done
echo $type
#############################
pushTmpDir ORG.organnot
if [[ ! "$1" =~ ^/ ]]; then
QUERY="${CALL_DIR}/$1"
else
......@@ -96,10 +96,12 @@ pushTmpDir ORG.organnot
RESULTS=$(basename ${QUERY/.*/})
LOG="${CALL_DIR}/${RESULTS}.log"
rm -f ${LOG}
openLogFile ${LOG}
case "$types" in
chloro)
loginfo "Annotating a plant chloroplast genome..."
......@@ -156,9 +158,9 @@ pushTmpDir ORG.organnot
exit 1
;;
*)
echo usage $0 1;;
usage $0 1;;
esac
if [[ "${organism}" == "no" ]]; then
organism="{organism}"
else
......
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