Bio/SeqIO/nexml.pm

   1 # BioPerl module for Bio::SeqIO::nexml
   2 #
   3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   4 #
   5 # Cared for by Chase Miller <chmille4@gmail.com>
   6 #
   7 # Copyright Chase Miller
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10 # _history
  11 # May, 2009  Largely written by Chase Miller
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::SeqIO::nexml - NeXML sequence input/output stream
  18
  19 =head1 SYNOPSIS
  20
  21 Do not use this module directly.  Use it via the Bio::SeqIO class.
  22
  23 =head1 DESCRIPTION
  24
  25 This object can transform Bio::Seq objects to and from NeXML format.
  26 For more information on the NeXML standard, visit L<http://www.nexml.org>.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to one
  34 of the Bioperl mailing lists.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 the bugs and their resolution.  Bug reports can be submitted via the
  54 web:
  55
  56   https://redmine.open-bio.org/projects/bioperl/
  57
  58 =head1 AUTHORS - Chase Miller
  59
  60 Email: chmille4@gmail.com
  61
  62 =head1 CONTRIBUTORS
  63
  64 Mark Jensen, maj@fortinbras.us
  65 Rutger Vos, rutgeraldo@gmail.com
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object
  70 methods. Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74 # Let the code begin...
  75
  76 package Bio::SeqIO::nexml;
  77
  78 use strict;
  79
  80 use lib '../..';
  81 use Bio::Seq;
  82 use Bio::Seq::SeqFactory;
  83 use Bio::Nexml::Factory;
  84 use Bio::Phylo::IO qw (parse unparse);
  85
  86 use base qw(Bio::SeqIO);
  87
  88 sub _initialize {
  89   my($self,@args) = @_;
  90   $self->SUPER::_initialize(@args);
  91   $self->{_doc} = undef;
  92 }
  93
  94 =head2 next_seq
  95
  96  Title   : next_seq
  97  Usage   : $seq = $stream->next_seq()
  98  Function: returns the next sequence in the stream
  99  Returns : L<Bio::Seq> object
 100  Args    : NONE
 101
 102 =cut
 103
 104 sub next_seq {
 105         my ($self) = @_;
 106     unless ( $self->{'_parsed'} ) {
 107         #use a parse function to load all the sequence objects found in the nexml file at once
 108         $self->_parse;
 109     }
 110     return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ];
 111 }
 112
 113 =head2 rewind
 114
 115  Title   : rewind
 116  Usage   : $seqio->rewind
 117  Function: Resets the stream
 118  Returns : none
 119  Args    : none
 120
 121
 122 =cut
 123
 124 sub rewind {
 125     my $self = shift;
 126     $self->{'_seqiter'} = 0;
 127 }
 128
 129 =head2 doc
 130
 131  Title   : doc
 132  Usage   : $treeio->doc
 133  Function: Returns the biophylo nexml document object
 134  Returns : Bio::Phylo::Project
 135  Args    : none or Bio::Phylo::Project object
 136
 137 =cut
 138
 139 sub doc {
 140         my ($obj,$value) = @_;
 141    if( defined $value) {
 142       $obj->{'_doc'} = $value;
 143         }
 144         return $obj->{'_doc'};
 145 }
 146
 147 sub _parse {
 148         my ($self) = @_;
 149         my $fac = Bio::Nexml::Factory->new();
 150
 151     $self->{'_parsed'}   = 1;
 152     $self->{'_seqiter'} = 0;
 153
 154         $self->doc(Bio::Phylo::IO->parse(
 155         '-file'       => $self->{'_file'},
 156         '-format'     => 'nexml',
 157         '-as_project' => '1'
 158         ));
 159
 160
 161
 162         $self->{'_seqs'} = $fac->create_bperl_seq($self);
 163
 164
 165         unless(@{ $self->{'_seqs'} } == 0)
 166         {
 167 #               self->debug("no seqs in $self->{_file}");
 168         }
 169  }
 170
 171
 172
 173
 174 =head2 write_seq
 175
 176  Title   : write_seq
 177  Usage   : $stream->write_seq(@seq)
 178  Function: Writes the $seq object into the stream
 179  Returns : 1 for success and 0 for error
 180  Args    : Array of 1 or more L<Bio::PrimarySeqI> objects
 181
 182 =cut
 183
 184 sub write_seq {
 185
 186         my ($self, $bp_seq) = @_;
 187
 188         my $fac = Bio::Nexml::Factory->new();
 189         my $taxa = $fac->create_bphylo_taxa($bp_seq);
 190         my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa);
 191
 192         my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type());
 193         $matrix->insert($seq);
 194         $matrix->set_taxa($taxa);
 195
 196         #set matrix label
 197         my $feat = ($bp_seq->get_SeqFeatures())[0];
 198         $matrix->set_name($feat->get_tag_values('matrix_label'));
 199
 200         $self->doc(Bio::Phylo::Factory->create_project());
 201
 202         $self->doc->insert($matrix);
 203
 204         my $ret = $self->_print($self->doc->to_xml());
 205         $self->flush;
 206         return $ret
 207 }
 208
 209
 210 1;