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

[Chris Fields]

Dave,

Is this using bioperl-live?  I recall this being a problem but I  
thought it was addressed in svn (and soon in the next point release).

chris

On Aug 14, 2009, at 9:10 AM, Dave Messina 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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