# BioPerl module for Bio::SeqIO::nexml
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chase Miller <chmille4@gmail.com>
#
# Copyright Chase Miller
#
# You may distribute this module under the same terms as perl itself
# _history
# May, 2009 Largely written by Chase Miller
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::nexml - NeXML sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from NeXML format.
For more information on the NeXML standard, visit L<http://www.nexml.org>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Chase Miller
Email: chmille4@gmail.com
=head1 CONTRIBUTORS
Mark Jensen, maj@fortinbras.us
Rutger Vos, rutgeraldo@gmail.com
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::nexml;
use strict;
use lib '../..';
use Bio::Seq;
use Bio::Seq::SeqFactory;
use Bio::Nexml::Factory;
use Bio::Phylo::IO qw (parse unparse);
use base qw(Bio::SeqIO);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
$self->{_doc} = undef;
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : L<Bio::Seq> object
Args : NONE
=cut
sub next_seq {
my ($self) = @_;
unless ( $self->{'_parsed'} ) {
#use a parse function to load all the sequence objects found in the nexml file at once
$self->_parse;
}
return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ];
}
=head2 rewind
Title : rewind
Usage : $seqio->rewind
Function: Resets the stream
Returns : none
Args : none
=cut
sub rewind {
my $self = shift;
$self->{'_seqiter'} = 0;
}
=head2 doc
Title : doc
Usage : $treeio->doc
Function: Returns the biophylo nexml document object
Returns : Bio::Phylo::Project
Args : none or Bio::Phylo::Project object
=cut
sub doc {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_doc'} = $value;
}
return $obj->{'_doc'};
}
sub _parse {
my ($self) = @_;
my $fac = Bio::Nexml::Factory->new();
$self->{'_parsed'} = 1;
$self->{'_seqiter'} = 0;
$self->doc(Bio::Phylo::IO->parse(
'-file' => $self->{'_file'},
'-format' => 'nexml',
'-as_project' => '1'
));
$self->{'_seqs'} = $fac->create_bperl_seq($self);
unless(@{ $self->{'_seqs'} } == 0)
{
# self->debug("no seqs in $self->{_file}");
}
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more L<Bio::PrimarySeqI> objects
=cut
sub write_seq {
my ($self, $bp_seq) = @_;
my $fac = Bio::Nexml::Factory->new();
my $taxa = $fac->create_bphylo_taxa($bp_seq);
my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa);
my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type());
$matrix->insert($seq);
$matrix->set_taxa($taxa);
#set matrix label
my $feat = ($bp_seq->get_SeqFeatures())[0];
$matrix->set_name($feat->get_tag_values('matrix_label'));
$self->doc(Bio::Phylo::Factory->create_project());
$self->doc->insert($matrix);
my $ret = $self->_print($self->doc->to_xml());
$self->flush;
return $ret
}
1;