branch-1-6/Bio/SeqIO/ztr.pm

   1 # $Id$
   2 # BioPerl module for Bio::SeqIO::ztr
   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::ztr - ztr 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 ztr 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 I<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.
  53 Bug reports can be submitted via the 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::ztr;
  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 => $self->verbose(), -type => 'Bio::Seq::Quality'));
  94   }
  95
  96   my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args);
  97   $compression = 2 unless defined $compression;
  98   $self->compression($compression);
  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, 'ztr');
 122
 123     # create the seq object
 124     $seq = $self->sequence_factory->create(-seq        => $seq,
 125                                            -id         => $id,
 126                                            -primary_id => $id,
 127                                            -desc       => $desc,
 128                                            -alphabet   => 'DNA',
 129                                            -qual       => $qual
 130                                            );
 131     return $seq;
 132 }
 133
 134 =head2 write_seq
 135
 136  Title   : write_seq
 137  Usage   : $stream->write_seq(@seq)
 138  Function: writes the $seq object into the stream
 139  Returns : 1 for success and 0 for error
 140  Args    : Bio::Seq object
 141
 142
 143 =cut
 144
 145 sub write_seq {
 146     my ($self,@seq) = @_;
 147
 148     my $fh = $self->_fh;
 149     foreach my $seq (@seq) {
 150         $self->write_trace($fh, $seq, 'ztr' . $self->compression);
 151     }
 152
 153     $self->flush if $self->_flush_on_write && defined $self->_fh;
 154     return 1;
 155 }
 156
 157 =head2 compression
 158
 159  Title   : compression
 160  Usage   : $stream->compression(3);
 161  Function: determines the level of ZTR compression
 162  Returns : the current (or newly set) value.
 163  Args    : 1, 2 or 3 - any other (defined) value will cause the compression
 164            to be reset to the default of 2.
 165
 166
 167 =cut
 168
 169 sub compression {
 170
 171     my ($self, $val) = @_;
 172
 173     if (defined $val) {
 174         if ($val =~ m/^1|2|3$/o) {
 175             $self->{_compression} = $val;
 176         } else {
 177             $self->{_compression} = 2;
 178         }
 179     }
 180
 181     return $self->{_compression};
 182 }
 183
 184 1;