[Bioperl-l] problems with Bio::Tools::GFF

[Lincoln Stein]

No, it is still tab delimited, but people consistently screw it up and it 
might be better to split on space, since spaces are no longer allowed in the 
columns.

Lincoln

On Monday 03 November 2003 12:41 pm, Scott Cain wrote:
> Hi Jason and Lincoln,
>
> I have a few concerns with Bio::Tools::GFF. The first is with the method
> _from_gff3_string, which does a split on \t to separate columns.  I
> think the GFF3 spec says it can be space delimited, so that should
> probably be \s+.  Additionally, to split the groups column, it uses
> \s*;\s*, but I think that spaces have to be escaped, therefore, it
> should only split on ; and spaces would indicate a problem (especially
> if one splits on spaces as indicated above).
>
> Finally, it doesn't provide a method of accessing the sequence that is
> optionally at the bottom of the file.  I am not exactly sure how to
> implement that (or I would), but I suspect it will have to be handled in
> the next_feature method.  Of course, the problem with handling it there
> is that it is not a feature.
>
> Scott

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
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