lib/Bio/SeqIO/ztr.pm

   1 # BioPerl module for Bio::SeqIO::ztr
   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::ztr - ztr 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 ztr 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::ztr;
  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 => $self->verbose(), -type => 'Bio::Seq::Quality'));
  93   }
  94
  95   my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args);
  96   $compression = 2 unless defined $compression;
  97   $self->compression($compression);
  98
  99   unless ($READ_AVAIL) {
 100       Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
 101                               -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
 102                             );
 103   }
 104 }
 105
 106 =head2 next_seq
 107
 108  Title   : next_seq
 109  Usage   : $seq = $stream->next_seq()
 110  Function: returns the next sequence in the stream
 111  Returns : Bio::Seq::Quality object
 112  Args    : NONE
 113
 114 =cut
 115
 116 sub next_seq {
 117
 118     my ($self) = @_;
 119
 120     my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr');
 121
 122     # create the seq object
 123     $seq = $self->sequence_factory->create(-seq        => $seq,
 124                                            -id         => $id,
 125                                            -primary_id => $id,
 126                                            -desc       => $desc,
 127                                            -alphabet   => 'DNA',
 128                                            -qual       => $qual
 129                                            );
 130     return $seq;
 131 }
 132
 133 =head2 write_seq
 134
 135  Title   : write_seq
 136  Usage   : $stream->write_seq(@seq)
 137  Function: writes the $seq object into the stream
 138  Returns : 1 for success and 0 for error
 139  Args    : Bio::Seq object
 140
 141
 142 =cut
 143
 144 sub write_seq {
 145     my ($self,@seq) = @_;
 146
 147     my $fh = $self->_fh;
 148     foreach my $seq (@seq) {
 149         $self->write_trace($fh, $seq, 'ztr' . $self->compression);
 150     }
 151
 152     $self->flush if $self->_flush_on_write && defined $self->_fh;
 153     return 1;
 154 }
 155
 156 =head2 compression
 157
 158  Title   : compression
 159  Usage   : $stream->compression(3);
 160  Function: determines the level of ZTR compression
 161  Returns : the current (or newly set) value.
 162  Args    : 1, 2 or 3 - any other (defined) value will cause the compression
 163            to be reset to the default of 2.
 164
 165
 166 =cut
 167
 168 sub compression {
 169
 170     my ($self, $val) = @_;
 171
 172     if (defined $val) {
 173         if ($val =~ m/^1|2|3$/o) {
 174             $self->{_compression} = $val;
 175         } else {
 176             $self->{_compression} = 2;
 177         }
 178     }
 179
 180     return $self->{_compression};
 181 }
 182
 183 1;