[Bioperl-l] fasta-formatted alignment used in SearchIO

[Jason Stajich]

What you have is a multiple sequence alignment, therefore you want to use
my $alnio = Bio::AlignIO(-format => 'fasta');
my $aln = $alnio->next_aln;


The SearchIO fasta module is for FastA search output, the AlignIO fasta
module is for fasta format MSA output.


HTH,
-jason
On Thu, 13 Feb 2003, Vladimir Babenko wrote:

>   Hello all,
>   I'm trying to use SearchIO module with
> fasta-formatted output of alignment in a form:
> >id1
> gccgccgcc---ccc
> >id2
> gccgccgccggg---
> >id3
> gccgccgcc---ccc
>
>   While invocationg SeqIO object:
> my $format='fasta';
> my $in = new Bio::SearchIO(-file   => $report,
> 			   -format => $format);
> and trying to read alignment:
> while( my $r = $in->next_result ) {
> ...}
>
>   I'm getting a warning:
> --------------------------------------
> MSG: unrecognized FASTA Family report file!
> --------------------------------------
>   Is it OK to use the abovementioned format or
> direct alignment output should be used as fasta?
>     Thank you,
>    Vladimir
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu