[Bioperl-l] Bio::Tools::GFF GFF3 parsing

[Lincoln Stein]

Hi Jason,

This is very good and I'm looking it over now.  Does it handle the CIGAR lines 
for gapped alignments?

Lincoln

On Thursday 18 September 2003 07:02 pm, Jason Stajich wrote:
> I added support for GFF3 parsing to Bio::Tools::GFF and added some simple
> tests.  I'm not 100% I have GFF3 output correct so Chris Mungall, Lincoln
> if you don't mind giving it a look over that would be great.  If I've
> duplicated functionality from somewhere else let me know, but I think
> Bio::Tools::GFF needs to be able to parse in GFF3 format at some point.
>
> The GFF3 parsing seems to work fine for processing the BGDP annotations so
> I feel confident it is working correctly, but more testing is welcomed!
>
> This is no real support for Unicode type output, the simpliest solution
> would be to rely on HTML::Entities for encoding non-ASCII codes.  I wasn't
> sure I wanted to make Tools::GFF depend on this right now so I've just
> implemented a simple encoding for '=,;'.  Feel free to fix this if it
> needs to be more aggresive.
>
> -jason

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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