[Bioperl-l] fasta program parsing

[Jason Stajich]

Yep the AlignIO::fasta expects sequence data - AlignIO is for
multiple sequence alignment data like clustal, gcg,msf, phylip, etc.

You want the Bio::SearchIO system for database search results.

my $out = new Bio::SearchIO(-format => 'fasta',
	                    -file   => 'filename')
while( my $report = $out->next_result ) {
 ... # see Bio::SearchIO documentation for more help
}

On Thu, 20 Jun 2002, Emig, Robin wrote:

> 	So I just tried to parse the output of the fasta program using
> the AlignIO::fasta, and it choked horribly, Why? because it was
> expecting a fasta formatted file alignment, not the output from FastA.
> Is there bioperl code to parse the output from FastA?

> -robin
> robin.emig@maxygen.com
> Bioinformatics Project Leader
> Maxygen, Inc
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu