package Bio::Phylo::Parsers::Taxlist;
use strict;
use base 'Bio::Phylo::Parsers::Abstract';
use Bio::Phylo::Util::CONSTANT;
=head1 NAME
Bio::Phylo::Parsers::Taxlist - Parser used by Bio::Phylo::IO, no serviceable parts inside
=head1 DESCRIPTION
This module is used for importing sets of taxa from plain text files, one taxon
on each line. It is called by the L<Bio::Phylo::IO|Bio::Phylo::IO> object, so
look there for usage examples. If you want to parse from a string, you
may need to indicate the field separator (default is '\n') to the
Bio::Phylo::IO->parse call:
-fieldsep => '\n',
=cut
sub _parse {
my $self = shift;
my $fh = $self->_handle;
my $fac = $self->_factory;
my $taxa = $fac->create_taxa;
local $/ = $self->_args->{'-fieldsep'} || "\n";
my $delim = $self->_args->{'-delim'} || "\t";
my @header;
LINE: while (<$fh>) {
chomp;
my @fields = split /$delim/, $_;
my $name;
my %meta;
# this means it is actually tabular, which also means it has a header
if ( scalar @fields > 1 ) {
# this happens the first line
if ( not @header ) {
@header = @fields;
for my $predicate ( @header ) {
if ( $predicate =~ /^(.+?):.+$/ ) {
my $prefix = $1;
$taxa->set_namespaces(
$prefix => $Bio::Phylo::Util::CONSTANT::NS->{$prefix}
);
}
}
next LINE;
}
# create key value pairs to attach
for my $i ( 1 .. $#fields ) {
$meta{$header[$i]} = $fields[$i] if $fields[$i];
}
}
# this is the first field regardless
$name = shift @fields;
my $taxon = $fac->create_taxon( '-name' => $name );
# attach metadata, if any
for my $predicate ( keys %meta ) {
$taxon->add_meta(
$fac->create_meta( '-triple' => { $predicate => $meta{$predicate} } )
);
}
$taxa->insert( $taxon );
}
return $taxa;
}
# 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 taxon list parser is called by the L<Bio::Phylo::IO> object.
Look there for examples.
=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;