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Bio-Phylo-v2.0.1
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

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

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

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63