[Bioperl-l] Re: BioPerl question

[Lincoln Stein]

Hi Nat,

The orthodox way is to create a Bio::AlignIO object using the desired output 
format and then to call write_aln() with the alignment object returned by 
SearchIO (via the next_algn() method).  However, your problem reading in the 
fasta alignment with AlignIO makes me nervous.  Can you amplify?

Lincoln

On Tuesday 02 July 2002 10:33 am, Nathan \(Nat\) Goodman wrote:
> Hi Lincoln and Chris
>
> I'm trying to use BioPerl (v 1.0.1 freshly downloaded today) to process
> fasta alignments.  This is just a toy example to get my feet wet with your
> awesome creation.
>
> I can read 'em in with SearchIO (but not AlignIO), but for the life of me I
> can't figure out how to print 'em back out.  What's the magic?
>
> I appreciate any help.
>
> Thanks very much,
> Nat

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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