Bio/SeqIO/pln.pm

   1 # BioPerl module for Bio::SeqIO::pln
   2 #
   3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   4 #
   5 # Cared for by Aaron Mackey <amackey@virginia.edu>
   6 #
   7 # Copyright Aaron Mackey
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::SeqIO::pln - pln trace sequence input/output stream
  16
  17 =head1 SYNOPSIS
  18
  19 Do not use this module directly.  Use it via the Bio::SeqIO class.
  20
  21 =head1 DESCRIPTION
  22
  23 This object can transform Bio::Seq objects to and from pln trace
  24 files.
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to one
  32 of the Bioperl mailing lists.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 I<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 the bugs and their resolution.
  52 Bug reports can be submitted via the web:
  53
  54   https://github.com/bioperl/bioperl-live/issues
  55
  56 =head1 AUTHORS - Aaron Mackey
  57
  58 Email: amackey@virginia.edu
  59
  60 =head1 APPENDIX
  61
  62 The rest of the documentation details each of the object
  63 methods. Internal methods are usually preceded with a _
  64
  65 =cut
  66
  67 # Let the code begin...
  68
  69 package Bio::SeqIO::pln;
  70 use vars qw(@ISA $READ_AVAIL);
  71 use strict;
  72
  73 use Bio::SeqIO;
  74 use Bio::Seq::SeqFactory;
  75
  76 push @ISA, qw( Bio::SeqIO );
  77
  78 sub BEGIN {
  79     eval { require Bio::SeqIO::staden::read; };
  80     if ($@) {
  81         $READ_AVAIL = 0;
  82     } else {
  83         push @ISA, "Bio::SeqIO::staden::read";
  84         $READ_AVAIL = 1;
  85     }
  86 }
  87
  88 sub _initialize {
  89   my($self,@args) = @_;
  90   $self->SUPER::_initialize(@args);
  91   if( ! defined $self->sequence_factory ) {
  92       $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));
  93   }
  94   unless ($READ_AVAIL) {
  95       Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
  96                               -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
  97                             );
  98   }
  99 }
 100
 101 =head2 next_seq
 102
 103  Title   : next_seq
 104  Usage   : $seq = $stream->next_seq()
 105  Function: returns the next sequence in the stream
 106  Returns : Bio::Seq::Quality object
 107  Args    : NONE
 108
 109 =cut
 110
 111 sub next_seq {
 112
 113     my ($self) = @_;
 114
 115     my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'pln');
 116
 117     # create the seq object
 118     $seq = $self->sequence_factory->create(-seq        => $seq,
 119                                            -id         => $id,
 120                                            -primary_id => $id,
 121                                            -desc       => $desc,
 122                                            -alphabet   => 'DNA',
 123                                            -qual       => $qual
 124                                            );
 125     return $seq;
 126 }
 127
 128 =head2 write_seq
 129
 130  Title   : write_seq
 131  Usage   : $stream->write_seq(@seq)
 132  Function: writes the $seq object into the stream
 133  Returns : 1 for success and 0 for error
 134  Args    : Bio::Seq object
 135
 136
 137 =cut
 138
 139 sub write_seq {
 140     my ($self,@seq) = @_;
 141
 142     my $fh = $self->_fh;
 143     foreach my $seq (@seq) {
 144         $self->write_trace($fh, $seq, 'pln');
 145     }
 146
 147     $self->flush if $self->_flush_on_write && defined $self->_fh;
 148     return 1;
 149 }
 150
 151 1;