[gt-users] gff3 parser

[Brent Pedersen]

On Fri, Feb 6, 2009 at 7:22 AM, Gordon Gremme <gremme at gmail.com> wrote:
>> ok. now i understand that problem, but not quite the solution.
>> where would it keep the GtCstrTable? as an additional field on the
>> GtGFF3Visitor struct?
>> or on the GtGFF3Instream?
>
> I would put it into the GtGFF3Visitor. That is, the IDs are changed
> when they are shown via the GtGFF3OutStream and not when they are read
> in via the GtGFF3InStream.
>
>
>> and then, the option will be a boolean in tools/gt_gff3.c like: -keepids
>
> Correct. I would pass it through to the GtGFF3Visitor similar to the
> method gt_gff3_out_stream_set_fasta_width().
>
>
>> so i think i can add an arg to gff3_parser.c
>> gt_gff3_parser_parse_genome_nodes and parse_regular_gff3_line
>> for the GtCstrTable *used_ids. then in parse_regular_gff3_line, it
>> modifies the id attribute if it's in used_ids already.
>
> No, I would rather put this functionality in the GtGFF3Vistitor (as
> described above).
>
> Happy coding,
>
> Gordon
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thanks, finally had time to try next iteration:
http://gist.github.com/61251

i'm doing something wrong with the make_unique_id function because
when it's called it does turn 'name' into 'name.1'
but it prints out ascii characters as well.
any feedback on that and in general?

thanks,
-brent