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corrected Annotation reordering for CDS

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Former-commit-id: c59ad42ebdd9772fbed5539388499840b57e3595
Former-commit-id: 5de4848d5d3b8e0d521120b7db92e145d9a6727f
This commit is contained in:
alain viari
2015-11-08 19:53:19 +01:00
parent 6fa63daf3f
commit 2d7006fd6c
1 changed files with 6 additions and 6 deletions
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12
org-annotate.sh
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@ -55,17 +55,17 @@ pushTmpDir ORG.organnot
loginfo "Done." loginfo "Done."
loginfo "Ordering annotations..." loginfo "Ordering annotations..."
awk '/^.....[^ ]/ { \ awk '/^.....(misc|repeat|rRNA|tRNA|gene)/ { \
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; \
print pos,$0} \ print pos,$0; \
/^..... / { \ next} \
pos++; \ { pos++; \
print pos,$0}' "${RESULTS}.annot" | \ print pos,$0}' "${RESULTS}.annot" | \
sort -nk1 | \ sort -nk1 |\
awk '{ \ awk '{ \
match($0,"^[0-9]* ");\ match($0,"^[0-9]* ");\
line=substr($0,RLENGTH+1,100000);\ line=substr($0,RLENGTH+1);\
print line}' print line}'
loginfo "Done." loginfo "Done."