[Biopython-dev] GFF file parsing and error handling

Brad Chapman chapmanb at 50mail.com
Tue Jan 10 16:21:17 UTC 2012


> I've got this GFF file ( placed in a spreadsheet for readability )
> https://docs.google.com/spreadsheet/ccc?key=0AtOqyz8P_fJ0dGVOMzNSM29qUVdjZmZ4emdIQ3U2OUE&hl=en_US#gid=0
> line 178 + 179 are the problematic lines
> what is going on here?

I'm not sure I understand exactly what is giving you problems. There are
two different genes:

- gene_id 000014 on segment human.ENr12. This has two exons and an
  annotated start and stop codon.

- gene_id 000001 on segment human.ENr13. This has an exon and a start
  codon, but no annotated stop codon.

Does that help?

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