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://github.com/bioperl/bioperl-live/issues
  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
 150     $self->{'_parsed'}  = 1;
 151     $self->{'_seqiter'} = 0;
 152     my $fac = Bio::Nexml::Factory->new();
 153
 154     # Only pass filename if filehandle is not available,
 155     # or "Bio::Phylo" will create a new filehandle that ends
 156     # out of scope and can't be closed directly, leaving 2 open
 157     # filehandles for the same file (so file can't be deleted)
 158     my $file_arg;
 159     my $file_value;
 160     if (     exists $self->{'_filehandle'}
 161         and defined $self->{'_filehandle'}
 162         ) {
 163         $file_arg   = '-handle';
 164         $file_value = $self->{'_filehandle'};
 165     }
 166     else {
 167         $file_arg   = '-file';
 168         $file_value = $self->{'_file'};
 169     }
 170
 171     $self->doc(Bio::Phylo::IO->parse(
 172                                      $file_arg     => $file_value,
 173                                      '-format'     => 'nexml',
 174                                      '-as_project' => '1'
 175                                      )
 176     );
 177     $self->{'_seqs'} = $fac->create_bperl_seq($self);
 178
 179     unless(@{ $self->{'_seqs'} } == 0) {
 180 #        self->debug("no seqs in $self->{_file}");
 181     }
 182 }
 183
 184 =head2 write_seq
 185
 186  Title   : write_seq
 187  Usage   : $stream->write_seq(@seq)
 188  Function: Writes the $seq object into the stream
 189  Returns : 1 for success and 0 for error
 190  Args    : Array of 1 or more L<Bio::PrimarySeqI> objects
 191
 192 =cut
 193
 194 sub write_seq {
 195
 196         my ($self, $bp_seq) = @_;
 197
 198         my $fac = Bio::Nexml::Factory->new();
 199         my $taxa = $fac->create_bphylo_taxa($bp_seq);
 200         my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa);
 201
 202         my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type());
 203         $matrix->insert($seq);
 204         $matrix->set_taxa($taxa);
 205
 206         #set matrix label
 207         my $feat = ($bp_seq->get_SeqFeatures())[0];
 208         $matrix->set_name($feat->get_tag_values('matrix_label'));
 209
 210         $self->doc(Bio::Phylo::Factory->create_project());
 211
 212         $self->doc->insert($matrix);
 213
 214         my $ret = $self->_print($self->doc->to_xml());
 215         $self->flush;
 216         return $ret
 217 }
 218
 219
 220 1;