package Bio::Phylo::Parsers::Table;
use strict;
use base 'Bio::Phylo::Parsers::Abstract';
=head1 NAME
Bio::Phylo::Parsers::Table - Parser used by Bio::Phylo::IO, no serviceable parts inside
=head1 DESCRIPTION
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 L<Bio::Phylo::IO|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'
=cut
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
=head1 SEE ALSO
There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo>
for any user or developer questions and discussions.
=over
=item L<Bio::Phylo::IO>
The table parser is called by the L<Bio::Phylo::IO|Bio::Phylo::IO> object.
Look there to learn how to parse tab- (or otherwise) delimited matrices.
=item L<Bio::Phylo::Manual>
Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>
=back
=head1 CITATION
If you use Bio::Phylo in published research, please cite it:
B<Rutger A Vos>, B<Jason Caravas>, B<Klaas Hartmann>, B<Mark A Jensen>
and B<Chase Miller>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I<BMC Bioinformatics> B<12>:63.
L<http://dx.doi.org/10.1186/1471-2105-12-63>
=cut
1;