PhyloSkims/annotate
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remove the printing of an extra empty line at the beginning of the embl

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Former-commit-id: bba6581b86f21474d6e9b2acb3a9b4937984bbb8
Former-commit-id: 7570b9c21814614c45e57e253bdfae58c9ba3c2b
This commit is contained in:
Eric Coissac
2016-05-02 12:25:05 +02:00
parent 8113b80d47
commit 8a1a1d57ba
1 changed files with 6 additions and 4 deletions
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8
org-annotate.sh
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@ -60,7 +60,7 @@ function usage {
if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@") if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
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
exit 1 usage $0 1
fi fi
eval set -- "$options" eval set -- "$options"
@ -82,11 +82,11 @@ do
shift shift
done done
echo $type
############################# #############################
pushTmpDir ORG.organnot pushTmpDir ORG.organnot
if [[ ! "$1" =~ ^/ ]]; then if [[ ! "$1" =~ ^/ ]]; then
QUERY="${CALL_DIR}/$1" QUERY="${CALL_DIR}/$1"
else else
@ -97,9 +97,11 @@ pushTmpDir ORG.organnot
RESULTS=$(basename ${QUERY/.*/}) RESULTS=$(basename ${QUERY/.*/})
LOG="${CALL_DIR}/${RESULTS}.log" LOG="${CALL_DIR}/${RESULTS}.log"
rm -f ${LOG} rm -f ${LOG}
openLogFile ${LOG} openLogFile ${LOG}
case "$types" in case "$types" in
chloro) chloro)
loginfo "Annotating a plant chloroplast genome..." loginfo "Annotating a plant chloroplast genome..."
@ -156,7 +158,7 @@ pushTmpDir ORG.organnot
exit 1 exit 1
;; ;;
*) *)
echo usage $0 1;; usage $0 1;;
esac esac
if [[ "${organism}" == "no" ]]; then if [[ "${organism}" == "no" ]]; then