Commit b78cd77b by Eric Coissac

Force source to be the first feature

parent c956dde7
...@@ -218,31 +218,31 @@ pushTmpDir ORG.organnot ...@@ -218,31 +218,31 @@ pushTmpDir ORG.organnot
loginfo "Done." loginfo "Done."
loginfo "Printing the source feature" loginfo "Printing the source feature"
echo "FT source 1..${sl}" >> "${RESULTS}.annot" echo "FT source 1..${sl}"
if [[ "${organism}" != "{organism}" ]] ; then if [[ "${organism}" != "{organism}" ]] ; then
echo "FT /organism=\"${organism}\"" >> "${RESULTS}.annot" echo "FT /organism=\"${organism}\""
fi fi
case "${types}" in case "${types}" in
chloro) chloro)
echo "FT /organelle=\"plastid:chloroplast\"" >> "${RESULTS}.annot" echo "FT /organelle=\"plastid:chloroplast\""
;; ;;
mito) mito)
echo "FT /organelle=\"mitochondrion\"" >> "${RESULTS}.annot" echo "FT /organelle=\"mitochondrion\""
;; ;;
*) *)
loginfo "Nuclear sequence" loginfo "Nuclear sequence"
;; ;;
esac esac
echo "FT /mol_type=\"genomic DNA\"" >> "${RESULTS}.annot" echo "FT /mol_type=\"genomic DNA\""
if [[ "${taxid}" != "no" ]] ; then if [[ "${taxid}" != "no" ]] ; then
echo "FT /db_xref=\"taxon:${taxid}\"" >> "${RESULTS}.annot" echo "FT /db_xref=\"taxon:${taxid}\""
fi fi
# echo "FT /country=\"Poland: Bialowieza Forest\"" >> "${RESULTS}.annot" # echo "FT /country=\"Poland: Bialowieza Forest\""
loginfo "Done." loginfo "Done."
loginfo "Ordering annotations..." loginfo "Ordering annotations..."
......
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