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

Bio-Phylo documentation Contained in the Bio-Phylo distribution.

Index

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NAME

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

DESCRIPTION

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This module is used to import data and taxa from plain text files or strings. The following additional argument must be used in the call to Bio::Phylo::IO:

 -type => (one of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS])

In addition, these arguments may be used to indicate line separators (default is "\n") and field separators (default is "\t"):

 -fieldsep => '\t',
 -linesep  => '\n'

SEE ALSO

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Bio::Phylo::IO

The table parser is called by the Bio::Phylo::IO object. Look there to learn how to parse tab- (or otherwise) delimited matrices.

Bio::Phylo::Manual

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

CITATION

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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

REVISION

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 $Id: Table.pm 1660 2011-04-02 18:29:40Z rvos $
Bio-Phylo documentation Contained in the Bio-Phylo distribution. 
# $Id: Table.pm 1660 2011-04-02 18:29:40Z rvos $
package Bio::Phylo::Parsers::Table;
use strict;
use base 'Bio::Phylo::Parsers::Abstract';


sub _parse {
    my $self = shift;
    my $fh   = $self->_handle;
    my $fac  = $self->_factory;
    my $type = $self->_args->{'-type'};
    local $/ = $self->_args->{'-linesep'} || "\n";
    my $sep    = $self->_args->{'-fieldsep'} || "\t";
    my $regex  = qr/$sep/;
    my $matrix = $fac->create_matrix( '-type' => $type );
    while (<$fh>) {
        chomp;
        my ( $name, @char ) = split $regex, $_;
        $matrix->insert(
            $fac->create_datum(
                '-type' => $type,
                '-name' => $name,
                '-char' => \@char,
            )
        );
    }
    return $matrix;
}

# podinherit_insert_token


1;