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

[Dave Messina]

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