File Coverage

Bio/SeqIO/raw.pm
Criterion Covered Total %
statement 32 45 71.1
branch 11 22 50.0
condition 5 11 45.4
subroutine 6 8 75.0
pod 3 3 100.0
total 57 89 64.0


line stmt bran cond sub pod time code
1             #-----------------------------------------------------------------------------
2             # PACKAGE : Bio::SeqIO::raw
3             # AUTHOR : Ewan Birney
4             # CREATED : Feb 16 1999
5             #
6             # Copyright (c) 1997-9 bioperl, Ewan Birney. All Rights Reserved.
7             # This module is free software; you can redistribute it and/or
8             # modify it under the same terms as Perl itself.
9             #
10             # _History_
11             #
12             # Ewan Birney developed the SeqIO
13             # schema and the first prototype modules.
14             #
15             # This code is based on his Bio::SeqIO::Fasta module with
16             # the necessary minor tweaks necessary to get it to read
17             # and write raw formatted sequences made by
18             # chris dagdigian
19             #
20             # October 18, 1999 Largely rewritten by Lincoln Stein
21             #
22             # Copyright Ewan Birney
23             #
24             # You may distribute this module under the same terms as perl itself
25              
26             # POD documentation - main docs before the code
27              
28             =head1 NAME
29              
30             Bio::SeqIO::raw - raw sequence file input/output stream
31              
32             =head1 SYNOPSIS
33              
34             Do not use this module directly. Use it via the L class.
35              
36             =head1 DESCRIPTION
37              
38             This object can transform Bio::Seq objects to and from raw flat
39             file databases.
40              
41             =head1 FEEDBACK
42              
43             =head2 Mailing Lists
44              
45             User feedback is an integral part of the evolution of this and other
46             Bioperl modules. Send your comments and suggestions preferably to one
47             of the Bioperl mailing lists. Your participation is much appreciated.
48              
49             bioperl-l@bioperl.org - General discussion
50             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
51              
52             =head2 Support
53              
54             Please direct usage questions or support issues to the mailing list:
55              
56             I
57              
58             rather than to the module maintainer directly. Many experienced and
59             reponsive experts will be able look at the problem and quickly
60             address it. Please include a thorough description of the problem
61             with code and data examples if at all possible.
62              
63             =head2 Reporting Bugs
64              
65             Report bugs to the Bioperl bug tracking system to help us keep track
66             the bugs and their resolution.
67             Bug reports can be submitted via the web:
68              
69             https://github.com/bioperl/bioperl-live/issues
70              
71             =head1 AUTHORS
72              
73             Ewan Birney Ebirney@ebi.ac.ukE
74             Lincoln Stein Elstein@cshl.orgE
75              
76             =head1 CONTRIBUTORS
77              
78             Jason Stajich Ejason@bioperl.org
79              
80             =head1 APPENDIX
81              
82             The rest of the documentation details each of the object methods.
83             Internal methods are usually preceded with a _
84              
85             =cut
86              
87              
88             # Let the code begin...
89              
90             package Bio::SeqIO::raw;
91 3     3   559 use strict;
  3         4  
  3         90  
92              
93 3     3   212 use Bio::Seq::SeqFactory;
  3         5  
  3         107  
94              
95 3     3   17 use base qw(Bio::SeqIO);
  3         5  
  3         1452  
96              
97             our %variant = ( 'multiple' => undef, # default
98             'single' => undef );
99              
100             sub _initialize {
101 11     11   23 my($self,@args) = @_;
102 11         35 $self->SUPER::_initialize(@args);
103 11         36 my ($variant) = $self->_rearrange([qw(VARIANT)], @args);
104 11   100     42 $variant ||= 'multiple';
105 11         36 $self->variant($variant);
106 11 100       41 $self->{record_separator} = $variant eq 'single' ? undef : $/;
107 11 50       38 if( ! defined $self->sequence_factory ) {
108 11         28 $self->sequence_factory(Bio::Seq::SeqFactory->new
109             (-verbose => $self->verbose(),
110             -type => 'Bio::Seq'));
111             }
112 11         38 $self->variant;
113             }
114              
115             =head2 next_seq
116              
117             Title : next_seq
118             Usage : $seq = $stream->next_seq()
119             Function: returns the next sequence in the stream
120             Returns : Bio::Seq object
121             Args :
122              
123              
124             =cut
125              
126             sub next_seq{
127 20     20 1 55 my ($self,@args) = @_;
128             ## When its 1 sequence per line with no formatting at all,
129             ## grabbing it should be easy :)
130            
131             ## adding an option to assume the file is one sequence
132 20         91 local $/ = $self->{record_separator};
133 20         73 my $nextline = $self->_readline();
134 20 100       48 return unless defined $nextline;
135            
136 18         42 my $sequence = uc($nextline);
137 18         109 $sequence =~ s/\W//g;
138 18 100       41 return unless $sequence;
139 17 50       58 return $self->sequence_factory->create(-seq => $sequence) if $sequence;
140             }
141              
142             =head2 write_seq
143              
144             Title : write_seq
145             Usage : $stream->write_seq($seq)
146             Function: writes the $seq object into the stream
147             Returns : 1 for success and 0 for error
148             Args : Array of Bio::PrimarySeqI objects
149              
150              
151             =cut
152              
153             sub write_seq {
154 5     5 1 27 my ($self,@seq) = @_;
155 5         11 foreach my $seq (@seq) {
156 5 50 33     36 $self->throw("Must provide a valid Bio::PrimarySeqI object")
      33        
157             unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
158 5 50       13 $self->_print($seq->seq, "\n") or return;
159             }
160 5 50 33     12 $self->flush if $self->_flush_on_write && defined $self->_fh;
161 5         11 return 1;
162             }
163              
164             =head2 write_qual
165              
166             Title : write_qual
167             Usage : $stream->write_qual($seq)
168             Function: writes the $seq object into the stream
169             Returns : 1 for success and 0 for error
170             Args : Bio::Seq::Quality object
171              
172              
173             =cut
174              
175             sub write_qual {
176 0     0 1   my ($self,@seq) = @_;
177 0           my @qual = ();
178 0           foreach (@seq) {
179 0 0         unless ($_->isa("Bio::Seq::Quality")){
180 0           warn("You cannot write raw qualities without supplying a Bio::Seq::".
181             "Quality object! You passed a ".ref($_)."\n");
182 0           next;
183             }
184 0           @qual = @{$_->qual};
  0            
185 0 0         if(scalar(@qual) == 0) {
186 0           $qual[0] = "\n";
187             }
188 0 0         $self->_print (join " ", @qual,"\n") or return;
189             }
190 0           return 1;
191             }
192              
193             =head2 variant
194              
195             Title : variant
196             Usage : $format = $obj->variant();
197             Function: Get and set method for the sequence variant. For raw sequence, this
198             indicates whether to treat the input as multiple sequences (the
199             default) or as a single sequence.
200              
201             Current values accepted are:
202              
203             'single' single sequence
204             'multiple' multiple sequences (default)
205             Returns : string
206             Args : new value, string
207              
208             =cut
209              
210             # variant() method inherited from Bio::Root::IO
211              
212             # private method for testing record separator
213              
214             sub _separator {
215 0     0     shift->{record_separator};
216             }
217              
218             1;