[Bioperl-l] Bio::SeqIO issue

[Chris Fields]

On Aug 6, 2009, at 11:51 AM, Peter wrote:

> On Thu, Aug 6, 2009 at 5:42 PM, Hilmar Lapp<hlapp at gmx.net> wrote:
>>
>>>> I agree with the not removing newlines in raw format being a bug.
>>>>
>>>>        -hilmar
>>>
>>> Acc. to the SeqIO::raw docs, this is a little trickier.  The  
>>> documented
>>> behavior explicitly indicates that each line (sans non-whitespace)  
>>> is
>>> assumed to be a separate sequence, so changing that behavior  
>>> breaks API.
>>
>> Ah - true indeed. I like the optional argument feature - that way  
>> it's easy
>> for the user to choose.
>>
>
> For reference, "raw" as a format in EMBOSS seems to give just one
> sequence regardless of any line breaks.

Yes, and that's the behavior I would expect, actually.

> Adding an optional argument might be clearest, but have you considered
> using the new BioPerl SeqIO variant argument to have two forms of raw
> (the original variant giving one sequence per line, and a new variant
> where you just get one sequence regardless of any line breaks)?
>
> Peter

That's a good point.  We'd have to keep 'raw' as the prior behavior,  
but 'raw-complete' could be used for such a circumstance ('raw-gulp'  
sounds just wrong ;)

chris