30 Oct 2017 19:50:35 UTC
- Distribution: Bio-Phylo
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- License: perl_5
- Perl: v5.8.0
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Bio::Phylo::Parsers::Fasta - Parser used by Bio::Phylo::IO, no serviceable parts inside
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.
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The fasta parser is called by the Bio::Phylo::IO object. Look there to learn more about parsing.
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