[Bioperl-l] Bio::SeqIO issue

[Peter]

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.

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