PhyloSkims/annotate
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Force source to be the first feature

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Former-commit-id: b78cd77b042bf3c7ec4251e5f2e77762b84d5995
Former-commit-id: 1f1ca1afd0359bd8fde039b8be0e80e9472124c7
This commit is contained in:
Eric Coissac
2016-10-09 07:19:00 -03:00
parent 8156d5dd2f
commit b3b9955140
1 changed files with 7 additions and 7 deletions
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14
org-annotate.sh
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@ -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..."