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Close #15. Actually the bug in intron location was related to a

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misinterpretation of the aragorn output format. Now tRNA, and intron
location are coherent with most of the locations extracted from genbank
file with one or 2 base pairs of difference.

Former-commit-id: dac4fb731e0edaeaebde9edc5350fce38ad99601
Former-commit-id: f8a0590342aec2db1fe5deb4475b8a9380891a48
This commit is contained in:
Eric Coissac
2015-12-18 08:39:04 +01:00
parent d09a1fc40a
commit cf54e7dcb1
1 changed files with 2 additions and 1 deletions
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3
detectors/trna/lib/aragorn_wrapper.awk
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@ -112,7 +112,8 @@ function emblTRNA(geneid,trna,loc,anti,intron,seq) {
intron=substr(intron,2,l-2); intron=substr(intron,2,l-2);
split(intron,intronpos,","); split(intron,intronpos,",");
ib=intronpos[1]; ib=intronpos[1];
ie=intronpos[2]; il=intronpos[2];
ie=ib+il-1;
match(loc,"[0-9][0-9]*"); match(loc,"[0-9][0-9]*");
gb=substr(loc,RSTART,RLENGTH); gb=substr(loc,RSTART,RLENGTH);
if (complement==0) { if (complement==0) {