[Bioperl-l] Converting between allowed SearchIO formats?
Jason Stajich
jason at bioperl.org
Tue Sep 22 16:07:14 UTC 2009
>>
>>
>> However, the above method does not work here. Is this for some deep
>> reason, or could the above method (based on the way SeqIO works) be
>> made to work? I'm guessing that the SearchIO object conversion is
>> simply harder to do than with SeqIO?
>
> This is something Jason could probably speak up on, but from my
> perspective it comes down to 'why?'. This opens up a very hard-to-
> implement door (converting to and from, for instance, BLAST to
> HMMER), which doesn't make sense from the end-user perspective.
> What most users want out of those formats is getting at the data in
> an easily accessible way, to further process them (filter, to GFF,
> etc), or to have them summarized. the Writer classes take care of
> the latter.
>
> There is a very generic, all-purpose write_result in Bio::SearchIO
> that just calls the a ResultWriter object (and dies if it isn't
> present). Note that this expects a ResultWriter, not a Hit/
> HSPWriter; it is write_result() after all. I think this kind of goes
> against the well-established API that exists with the other
> write_foo implementations for the IO classes, where the input/output
> format should match, but there you have it.
>
Dan -
I'm confused about what you are trying to do or what is broken - are
you just annoyed that the API isn't the same style as Bio::SeqIO.
--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
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