[gt-users] gff3 parser

[Brent Pedersen]

On Tue, Feb 17, 2009 at 11:40 AM, Brent Pedersen <bpederse at gmail.com> wrote:
> 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
>

now with tests:
http://gist.github.com/62770