Bio/SeqIO/exp.pm

   1 # $Id$
   2 # BioPerl module for Bio::SeqIO::exp
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Aaron Mackey <amackey@virginia.edu>
   7 #
   8 # Copyright Aaron Mackey
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqIO::exp - exp trace sequence input/output stream
  17
  18 =head1 SYNOPSIS
  19
  20 Do not use this module directly.  Use it via the Bio::SeqIO class.
  21
  22 =head1 DESCRIPTION
  23
  24 This object can transform Bio::Seq objects to and from exp trace
  25 files.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to one
  33 of the Bioperl mailing lists.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 L<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the
  53 web:
  54
  55   http://bugzilla.open-bio.org/
  56
  57 =head1 AUTHORS - Aaron Mackey
  58
  59 Email: amackey@virginia.edu
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object
  64 methods. Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68 # Let the code begin...
  69
  70 package Bio::SeqIO::exp;
  71 use vars qw(@ISA $READ_AVAIL);
  72 use strict;
  73
  74 use Bio::SeqIO;
  75 use Bio::Seq::SeqFactory;
  76
  77 push @ISA, qw( Bio::SeqIO );
  78
  79 sub BEGIN {
  80     eval { require Bio::SeqIO::staden::read; };
  81     if ($@) {
  82         $READ_AVAIL = 0;
  83     } else {
  84         push @ISA, "Bio::SeqIO::staden::read";
  85         $READ_AVAIL = 1;
  86     }
  87 }
  88
  89 sub _initialize {
  90   my($self,@args) = @_;
  91   $self->SUPER::_initialize(@args);
  92   if( ! defined $self->sequence_factory ) {
  93       $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));
  94   }
  95   unless ($READ_AVAIL) {
  96       Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
  97                               -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
  98                             );
  99   }
 100 }
 101
 102 =head2 next_seq
 103
 104  Title   : next_seq
 105  Usage   : $seq = $stream->next_seq()
 106  Function: returns the next sequence in the stream
 107  Returns : Bio::Seq::Quality object
 108  Args    : NONE
 109
 110 =cut
 111
 112 sub next_seq {
 113
 114     my ($self) = @_;
 115
 116     my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'exp');
 117
 118     # create the seq object
 119     $seq = $self->sequence_factory->create(-seq        => $seq,
 120                                            -id         => $id,
 121                                            -primary_id => $id,
 122                                            -desc       => $desc,
 123                                            -alphabet   => 'DNA',
 124                                            -qual       => $qual
 125                                            );
 126     return $seq;
 127 }
 128
 129 =head2 write_seq
 130
 131  Title   : write_seq
 132  Usage   : $stream->write_seq(@seq)
 133  Function: writes the $seq object into the stream
 134  Returns : 1 for success and 0 for error
 135  Args    : Bio::Seq object
 136
 137
 138 =cut
 139
 140 sub write_seq {
 141     my ($self,@seq) = @_;
 142
 143     my $fh = $self->_fh;
 144     foreach my $seq (@seq) {
 145         $self->write_trace($fh, $seq, 'exp');
 146     }
 147
 148     $self->flush if $self->_flush_on_write && defined $self->_fh;
 149     return 1;
 150 }
 151
 152 1;