/ 
Bio-Phylo-0.34
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Parsers::Fasta

NAME

Bio::Phylo::Parsers::Fasta - Parser used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION

A very symplistic FASTA file parser. To use it, you need to pass an argument that specifies the data type of the FASTA records into the parse function, i.e.

my $project = parse(
   -type   => 'dna', # or rna, protein
   -format => 'fasta',
   -file   => 'infile.fa',
   -as_project => 1
);

For each FASTA record, the first "word" on the definition line is used as the name of the produced datum object. The entire line is assigned to:

$datum->set_generic( 'fasta_def_line' => $line )

So you can retrieve it by calling:

my $line = $datum->get_generic('fasta_def_line');

BioPerl actually parses definition lines to get GIs and such out of there, so if you're looking for that, use Bio::SeqIO from the bioperl-live distribution. You can always pass the resulting Bio::Seq objects to Bio::Phylo::Matrices::Datum->new_from_bioperl to turn the Bio::Seq objects that Bio::SeqIO produces into Bio::Phylo::Matrices::Datum objects.

SEE ALSO

Bio::Phylo::IO

The fasta parser is called by the Bio::Phylo::IO object. Look there to learn more about parsing.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com

REVISION

$Id: Table.pm 1524 2010-11-25 19:24:12Z rvos $