|
0
|
1 # $Id: exp.pm,v 1.8 2002/10/22 07:38:42 lapp Exp $
|
|
|
2 # BioPerl module for Bio::SeqIO::exp
|
|
|
3 #
|
|
|
4 # Cared for by Aaron Mackey <amackey@virginia.edu>
|
|
|
5 #
|
|
|
6 # Copyright Aaron Mackey
|
|
|
7 #
|
|
|
8 # You may distribute this module under the same terms as perl itself
|
|
|
9
|
|
|
10 # POD documentation - main docs before the code
|
|
|
11
|
|
|
12 =head1 NAME
|
|
|
13
|
|
|
14 Bio::SeqIO::exp - exp trace sequence input/output stream
|
|
|
15
|
|
|
16 =head1 SYNOPSIS
|
|
|
17
|
|
|
18 Do not use this module directly. Use it via the Bio::SeqIO class.
|
|
|
19
|
|
|
20 =head1 DESCRIPTION
|
|
|
21
|
|
|
22 This object can transform Bio::Seq objects to and from exp trace
|
|
|
23 files.
|
|
|
24
|
|
|
25 =head1 FEEDBACK
|
|
|
26
|
|
|
27 =head2 Mailing Lists
|
|
|
28
|
|
|
29 User feedback is an integral part of the evolution of this and other
|
|
|
30 Bioperl modules. Send your comments and suggestions preferably to one
|
|
|
31 of the Bioperl mailing lists. Your participation is much appreciated.
|
|
|
32
|
|
|
33 bioperl-l@bioperl.org - General discussion
|
|
|
34 http://bioperl.org/MailList.shtml - About the mailing lists
|
|
|
35
|
|
|
36 =head2 Reporting Bugs
|
|
|
37
|
|
|
38 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
39 the bugs and their resolution.
|
|
|
40 Bug reports can be submitted via email or the web:
|
|
|
41
|
|
|
42 bioperl-bugs@bio.perl.org
|
|
|
43 http://bugzilla.bioperl.org/
|
|
|
44
|
|
|
45 =head1 AUTHORS - Aaron Mackey
|
|
|
46
|
|
|
47 Email: amackey@virginia.edu
|
|
|
48
|
|
|
49 =head1 APPENDIX
|
|
|
50
|
|
|
51 The rest of the documentation details each of the object
|
|
|
52 methods. Internal methods are usually preceded with a _
|
|
|
53
|
|
|
54 =cut
|
|
|
55
|
|
|
56 # Let the code begin...
|
|
|
57
|
|
|
58 package Bio::SeqIO::exp;
|
|
|
59 use vars qw(@ISA $READ_AVAIL);
|
|
|
60 use strict;
|
|
|
61 # Object preamble - inherits from Bio::Root::Object
|
|
|
62
|
|
|
63 use Bio::SeqIO;
|
|
|
64 use Bio::Seq::SeqFactory;
|
|
|
65
|
|
|
66 push @ISA, qw( Bio::SeqIO );
|
|
|
67
|
|
|
68 sub BEGIN {
|
|
|
69 eval { require Bio::SeqIO::staden::read; };
|
|
|
70 if ($@) {
|
|
|
71 $READ_AVAIL = 0;
|
|
|
72 } else {
|
|
|
73 push @ISA, "Bio::SeqIO::staden::read";
|
|
|
74 $READ_AVAIL = 1;
|
|
|
75 }
|
|
|
76 }
|
|
|
77
|
|
|
78 sub _initialize {
|
|
|
79 my($self,@args) = @_;
|
|
|
80 $self->SUPER::_initialize(@args);
|
|
|
81 if( ! defined $self->sequence_factory ) {
|
|
|
82 $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality'));
|
|
|
83 }
|
|
|
84 unless ($READ_AVAIL) {
|
|
|
85 Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
|
|
|
86 -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
|
|
|
87 );
|
|
|
88 }
|
|
|
89 }
|
|
|
90
|
|
|
91 =head2 next_seq
|
|
|
92
|
|
|
93 Title : next_seq
|
|
|
94 Usage : $seq = $stream->next_seq()
|
|
|
95 Function: returns the next sequence in the stream
|
|
|
96 Returns : Bio::SeqWithQuality object
|
|
|
97 Args : NONE
|
|
|
98
|
|
|
99 =cut
|
|
|
100
|
|
|
101 sub next_seq {
|
|
|
102
|
|
|
103 my ($self) = @_;
|
|
|
104
|
|
|
105 my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'exp');
|
|
|
106
|
|
|
107 # create the seq object
|
|
|
108 $seq = $self->sequence_factory->create(-seq => $seq,
|
|
|
109 -id => $id,
|
|
|
110 -primary_id => $id,
|
|
|
111 -desc => $desc,
|
|
|
112 -alphabet => 'DNA',
|
|
|
113 -qual => $qual
|
|
|
114 );
|
|
|
115 return $seq;
|
|
|
116 }
|
|
|
117
|
|
|
118 =head2 write_seq
|
|
|
119
|
|
|
120 Title : write_seq
|
|
|
121 Usage : $stream->write_seq(@seq)
|
|
|
122 Function: writes the $seq object into the stream
|
|
|
123 Returns : 1 for success and 0 for error
|
|
|
124 Args : Bio::Seq object
|
|
|
125
|
|
|
126
|
|
|
127 =cut
|
|
|
128
|
|
|
129 sub write_seq {
|
|
|
130 my ($self,@seq) = @_;
|
|
|
131
|
|
|
132 my $fh = $self->_fh;
|
|
|
133 foreach my $seq (@seq) {
|
|
|
134 $self->write_trace($fh, $seq, 'exp');
|
|
|
135 }
|
|
|
136
|
|
|
137 $self->flush if $self->_flush_on_write && defined $self->_fh;
|
|
|
138 return 1;
|
|
|
139 }
|
|
|
140
|
|
|
141 1;
|
