1 # BioPerl module for Bio::SeqIO::ztr
3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
5 # Cared for by Aaron Mackey <amackey@virginia.edu>
7 # Copyright Aaron Mackey
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::SeqIO::ztr - ztr trace sequence input/output stream
19 Do not use this module directly. Use it via the Bio::SeqIO class.
23 This object can transform Bio::Seq objects to and from ztr trace
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.
34 bioperl-l@bioperl.org - General discussion
35 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
39 Please direct usage questions or support issues to the mailing list:
41 I<bioperl-l@bioperl.org>
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.
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:
54 https://redmine.open-bio.org/projects/bioperl/
56 =head1 AUTHORS - Aaron Mackey
58 Email: amackey@virginia.edu
62 The rest of the documentation details each of the object
63 methods. Internal methods are usually preceded with a _
67 # Let the code begin...
69 package Bio
::SeqIO
::ztr
;
70 use vars
qw(@ISA $READ_AVAIL);
74 use Bio::Seq::SeqFactory;
76 push @ISA, qw( Bio::SeqIO );
79 eval { require Bio
::SeqIO
::staden
::read; };
83 push @ISA, "Bio::SeqIO::staden::read";
90 $self->SUPER::_initialize
(@args);
91 if( ! defined $self->sequence_factory ) {
92 $self->sequence_factory(Bio
::Seq
::SeqFactory
->new(-verbose
=> $self->verbose(), -type
=> 'Bio::Seq::Quality'));
95 my ($compression) = $self->_rearrange([qw
[COMPRESSION
]], @args);
96 $compression = 2 unless defined $compression;
97 $self->compression($compression);
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!"
109 Usage : $seq = $stream->next_seq()
110 Function: returns the next sequence in the stream
111 Returns : Bio::Seq::Quality object
120 my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr');
122 # create the seq object
123 $seq = $self->sequence_factory->create(-seq
=> $seq,
136 Usage : $stream->write_seq(@seq)
137 Function: writes the $seq object into the stream
138 Returns : 1 for success and 0 for error
139 Args : Bio::Seq object
145 my ($self,@seq) = @_;
148 foreach my $seq (@seq) {
149 $self->write_trace($fh, $seq, 'ztr' . $self->compression);
152 $self->flush if $self->_flush_on_write && defined $self->_fh;
159 Usage : $stream->compression(3);
160 Function: determines the level of ZTR compression
161 Returns : the current (or newly set) value.
162 Args : 1, 2 or 3 - any other (defined) value will cause the compression
163 to be reset to the default of 2.
170 my ($self, $val) = @_;
173 if ($val =~ m/^1|2|3$/o) {
174 $self->{_compression
} = $val;
176 $self->{_compression
} = 2;
180 return $self->{_compression
};