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Manual Reference Pages  -  BIO::PHYLO::PARSERS::FASTA (3)

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NAME

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

CONTENTS

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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::PARSERS::FASTA (3) 2014-02-08

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