[Biopython-dev] GFF parser bug?

[Peter]

On Mon, Apr 26, 2010 at 12:09 AM, Eli Papa <elipapa at mit.edu> wrote:
> Hello,
>
> While trying to use the GFF parser I ran into a value error.
>
> I think it's probably due to one of the GFF3 fields in my file not being
> specified as 'key=value', but just as 'value'.
>
> Hope this helps,
> eli
>
> ...
> The gff file is as follows:
>
> ##gff-version 3
> ##sequence-region scaffold4215_3 1 6526
> scaffold4215_3  glimmer gene    3       62      .       -       .
>  ID=GL0000006;Name=GL0000006;Lack 3'-end;
> scaffold4215_3  glimmer mRNA    3       62      .       -       .
>  ID=GL0000006;Name=GL0000006;Parent=GL0000006;Lack 3'-end;
> scaffold4215_3  glimmer CDS     3       62      2.84    -       0
>  Parent=GL0000006;Lack 3'-end;
> scaffold4215_3  glimmer gene    124     1983    .       -       .
>  ID=GL0000007;Name=GL0000007;Complete;
> [...]

Hi Eli,

Where did this GFF3 file come from? The final column looks invalid to me
(it should be a list of key=value; statements). The specification seems
quite clear on this: http://www.sequenceontology.org/gff3.shtml

Regards,

Peter