[gt-users] gff3 parser

[Brent Pedersen]

On Tue, Feb 17, 2009 at 8:07 AM, Gordon Gremme <gremme at gmail.com> wrote:
>>> bah. i was trying to avoid becoming a c programmer.
>
> It doesn't hurt to know some C, all major scripting languages are
> written in it ;-)
>
>
>>>>> should i just change the tests or do you want to keep the original behavior when
>>>>> the retainids is not used?
>>>> Please keep the original behaviour.
>>> ok. all tests pass with this patch:
>>> http://gist.github.com/62770/
>
> Cool!
>
>
>> We should maybe generally discuss whether ID renaming may be
>> counterproductive in the case of multi-line features, e.g.
>>
>> $ bin/gt gff3 -retainids testdata/multi_feature_simple.gff3
>> ##gff-version   3
>> ##sequence-region   ctg123 1 1497228
>> warning: feature ID "CDS1" not unique: changing to CDS1.1
>> ctg123  .       gene    1000    9000    .       +       .       ID=gene1
>> ctg123  .       CDS     1201    1500    .       +       0       ID=CDS1;Parent=gene1
>> ctg123  .       CDS     3000    3902    .       +       0       ID=CDS1.1;Parent=gene1
>>
>> breaks the "same-ID" rule for the multi-line features. I am not sure
>> whether this may lead to problems or not...
>> Any comments?
>
> Good point Sascha, that is a bug in the new retainids functionality.
> Multi-features have to be handled explicitly (similar to the
> non-retainids case) to avoid this problem.
>
> I think after fixing this and two additonal -retainids test (one for
> ``normal'' features and one for multi-features) we are ready for prime
> time!
>
> Gordon
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ok. i'll update to handle these cases and add tests. i'm just joking
about learning C.
-b