PhyloSkims/annotate
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Makes modification on the sequence header and feature source

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Former-commit-id: 10e921644ed414771a4d5c5017425c53b83e31c7
Former-commit-id: 5b05b011222f74c784f36f99d111e74b5402ccdd
This commit is contained in:
Eric Coissac
2021-11-05 09:30:55 +01:00
parent 616d5d084b
commit 9648bbb874
1 changed files with 5 additions and 4 deletions
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9
org-annotate.sh
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@ -435,10 +435,11 @@ pushTmpDir ORG.organnot
echo "XX" echo "XX"
echo "PR Project:${project};" echo "PR Project:${project};"
echo "XX" echo "XX"
echo "DE XXX"
else
split80 "${organism} ${defline}." "DE "
fi fi
split80 "${organism} ${defline}." "DE "
echo "DE "
echo "XX" echo "XX"
loginfo "Done." loginfo "Done."
@ -482,9 +483,9 @@ pushTmpDir ORG.organnot
loginfo "Done." loginfo "Done."
loginfo "Ordering annotations..." loginfo "Ordering annotations..."
$AwkCmd '(entry && /^.....(misc|repeat|rRNA|tRNA|gene|source)/) { \ $AwkCmd '(entry && /^.....(misc|repeat|rRNA|tRNA|CDS|source)/) { \
print pos,entry } \ print pos,entry } \
/^.....(misc|repeat|rRNA|tRNA|gene|source)/ { \ /^.....(misc|repeat|rRNA|tRNA|CDS|source)/ { \
match($3,"[0-9][0-9]*"); \ match($3,"[0-9][0-9]*"); \
pos=substr($3,RSTART,RLENGTH)*1000 + 1; \ pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
entry=$0; \ entry=$0; \