[Bioperl-l] SimpleAlign is_flush

[Chris Fields]

That's true.  I assumed Bernd's seqs were aligned.

chris

On Dec 5, 2007, at 8:56 AM, aaron.j.mackey at gsk.com wrote:

> Well, if you use AlignIO::fasta to read in a multi-fasta file of
> *unaligned* sequences, AlignIO::fasta makes the assumption that all of
> your sequences are aligned, and pads the ends of shorter sequences  
> with
> gap characters (essentially, enforcing a rather silly, yet valid
> alignment).  The fact that is_flush() then returns 1 is secondary.
>
> If you just want to read in an array of unaligned sequences, use
> SeqIO::fasta instead.  It doesn't really make much sense to use  
> AlignIO
> for sequences that are not aligned ... conversely, if you *do* have
> aligned sequences in a multi-fasta file, then it does make sense to  
> use
> AlignIO, and it also makes sense for AlignIO::fasta to end-pad  
> sequences
> with gaps as necessary to get a fully valid, flush multiple sequence
> alignment matrix.
>
> -Aaron
>
> bioperl-l-bounces at lists.open-bio.org wrote on 12/05/2007 08:53:59 AM:
>
>> 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.
>>
>> chris
>>
>> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign