[Bioperl-l] SimpleAlign is_flush

Chris Fields cjfields at uiuc.edu
Wed Dec 5 08:53:59 EST 2007

Yes; it's a convenient way to make sure all seqs have the same length  
(including gaps).  Nice for checking when adding new seqs to an  
alignment or building new parsers.


On Dec 5, 2007, at 7:10 AM, Bernd Web wrote:

> Hi,
> SimpleAlign has an is_flush:
> Function  : Tells you whether the alignment is flush, i.e. all of the
> same length
> Returns   : 1 or 0
> I  noticed that a file with multiple fasta sequences with different
> lengths has an is_flush  value of 1. Printing the "alignment" shows
> that sequences are appended with "-" so that the all are the same
> length. Does this mean that is_flush for alignments read in via
> AlignIO is indeed always true and thus as such a so useful ?
> (using bioperl version: 1.005002102)
> Regards,
> Bernd
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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