parse simple returns different start location

[Barbora Nétková]

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

  in_file = "your_file.gff"
  in_handle = open(in_file)

  for record in GFF.parse_simple(in_handle):
        print record['type']
        print record['id']
        print record['location']

  in_handle.close()

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.

[Brad Chapman]

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.

[Barbora Nétková]

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 :)