Bio/SeqIO/abi.pm

   1 # $Id$
   2 # BioPerl module for Bio::SeqIO::abi
   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::abi - abi 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 abi trace
  25 files.  To optionally read the trace graph data (which can be used
  26 to draw chromatographs, for instance), set the optional
  27 '-read_graph_data' flag or the read_graph_data method to a value
  28 evaluating to TRUE.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to one
  36 of the Bioperl mailing lists.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 L<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 the bugs and their resolution.
  56 Bug reports can be submitted via the web:
  57
  58   http://bugzilla.open-bio.org/
  59
  60 =head1 AUTHORS - Aaron Mackey
  61
  62 Email: amackey@virginia.edu
  63
  64 =head1 APPENDIX
  65
  66 The rest of the documentation details each of the object
  67 methods. Internal methods are usually preceded with a _
  68
  69 =cut
  70
  71 # Let the code begin...
  72
  73 package Bio::SeqIO::abi;
  74 use vars qw(@ISA $READ_AVAIL);
  75 use strict;
  76
  77 use Bio::SeqIO;
  78 use Bio::Seq::SeqFactory;
  79
  80 push @ISA, qw( Bio::SeqIO );
  81
  82 sub BEGIN {
  83     eval { require Bio::SeqIO::staden::read; };
  84     if ($@) {
  85         $READ_AVAIL = 0;
  86     } else {
  87         push @ISA, "Bio::SeqIO::staden::read";
  88         $READ_AVAIL = 1;
  89     }
  90 }
  91
  92 sub _initialize {
  93   my($self,@args) = @_;
  94   $self->SUPER::_initialize(@args);
  95   my ($get_trace) = $self->_rearrange([qw(get_trace_data)],@args);
  96   $get_trace && $self->get_trace_data(1);
  97   if( ! defined $self->sequence_factory ) {
  98       $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));
  99   }
 100   unless ($READ_AVAIL) {
 101       Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
 102                               -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
 103                             );
 104   }
 105 }
 106
 107 =head2 next_seq
 108
 109  Title   : next_seq
 110  Usage   : $seq = $stream->next_seq()
 111  Function: returns the next sequence in the stream
 112  Returns : Bio::Seq::Quality object
 113  Args    : NONE
 114
 115 =cut
 116
 117 sub next_seq {
 118
 119     my ($self) = @_;
 120
 121     my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'abi');
 122
 123     # create the seq object
 124         my ($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height);
 125         if ($self->get_trace_data) {
 126                 ($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height) = $self->read_trace_with_graph($self->_fh, 'abi');
 127         } else {
 128                 $base_locs = [];
 129         }
 130
 131     # create the seq object
 132     $seq = $self->sequence_factory->create(-seq        => $seq,
 133                                            -id         => $id,
 134                                            -primary_id => $id,
 135                                            -desc       => $desc,
 136                                            -alphabet   => 'DNA',
 137                                            -qual       => $qual,
 138                                            -trace      => join (" ", @{$base_locs}),
 139                                            -trace_data => { a_trace => $a_trace,
 140                                                                            c_trace => $c_trace,
 141                                                                            g_trace => $g_trace,
 142                                                                            t_trace => $t_trace,
 143                                                             max_height => $max_height,
 144                                                                 num_points => $points }
 145                                            );
 146     return $seq;
 147 }
 148
 149 =head2 write_seq
 150
 151  Title   : write_seq
 152  Usage   : $stream->write_seq(@seq)
 153  Function: writes the $seq object into the stream
 154  Returns : 1 for success and 0 for error
 155  Args    : Bio::Seq object
 156
 157
 158 =cut
 159
 160 sub write_seq {
 161     my ($self,@seq) = @_;
 162
 163     my $fh = $self->_fh;
 164     foreach my $seq (@seq) {
 165         $self->write_trace($fh, $seq, 'abi');
 166     }
 167
 168     $self->flush if $self->_flush_on_write && defined $self->_fh;
 169     return 1;
 170 }
 171
 172 =head2 get_trace_data
 173
 174  Title   : get_trace_data
 175  Usage   : $stream->get_trace_data(1)
 176  Function: set boolean flag to retrieve the trace data (possibly for
 177            output)
 178  Returns : bool value, TRUE = retrieve trace data (default FALSE)
 179  Args    : bool value
 180
 181 =cut
 182
 183 sub get_trace_data {
 184         my ($self, $val) = @_;
 185         $self->{_get_trace_data} = $val ? 1 : 0;
 186         $self->{_get_trace_data};
 187 }
 188
 189 1;