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| Bio::Phylo::Parsers::Fasta(3) | User Contributed Perl Documentation | Bio::Phylo::Parsers::Fasta(3) |
NAME
Bio::Phylo::Parsers::Fasta - Parser used by Bio::Phylo::IO, no serviceable parts insideDESCRIPTION
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>
| 2017-10-30 | perl v5.32.1 |
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