[Bioperl-l] AlignIO error with aligments containing an all-gap sequence

[Bernd Web]

Hi Dave,

I have observed the same (with bioperl 1.52) for the same reason. It
would be nice not to have these errors as also in my view an all-gaps
sequence is a sequence. I also found that sometimes parsing such
alignments fails when the all-gaps sequence is the last in the
alignment (bug 2744, in Bio::LocatableSeq).


Regards,
Bernd

On Fri, Aug 14, 2009 at 4:10 PM, Dave Messina<David.Messina at sbc.su.se> wrote:
> Hi everyone,
> I'm using Bio::AlignIO to read in a series of multiple alignments.
> Occasionally, an alignment will have a sequence which consists entirely of
> gaps (these are actually trimmed sub-alignments; that's why).
>
> Each time I read in such an alignment, an error will be raised when the
> Bio::LocatableSeq object is created for the all-gap sequence (actually, the
> error comes from the superclass Bio::PrimarySeq).
>
> To my way of thinking, an alignment is not invalid if it contains such
> all-gap sequences, so there shouldn't be an error. This could be done by
> having Bio::AlignIO::* passing the -nowarnonempty flag when creating the
> sequence objects.
>
> Any thoughts on this? Is there a better way to suppress the warning than
> changing the behavior of all the AlignIO modules?
>
>
> Dave
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