Closed NtBaru closed 10 years ago
Thanks for using the GFF module and sorry for any confusion. The library follows the Biopython conventions of using 0-based coordinates internally, which is identical to the normal slicing coordinates that Python itself uses. GFF is a 1-based coordinate system, so the difference you're seeing is due to handling that conversion which happens on import/export to GFF.
This is a nice general discussion about the difference between zero and 1-based coordinate systems:
http://www.biostars.org/p/6373/
Hope this helps.
I didn't know about this difference before, its my first project in the field of bioinformatics. Thanks a lot for explanation, it was really helpful :)
I need to parse GFF file and I found a little problem.
In my GFF file is (for example) this line: BAC1_SV_50C14_semf_p2_contig1 ltr LTR_retrotransposon 38 9461 0 . 0 ID=ele00002;
So the location should be [38, 9461], but parse_simple(...) returns location [37, 9461]. It happened in all files I tried.
My code look like this: from BCBio import GFF
Ant it prints this: LTR_retrotransposon ele00002 [37, 9461]
Can someone explain me what is wrong please? I don know if it is on purpose or if it is some bug.