[Bioperl-l] Converting between allowed SearchIO formats?

[Jason Stajich]

>>
>>
>> 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