File Coverage

Bio/SeqIO/largefasta.pm
Criterion Covered Total %
statement 50 54 92.5
branch 12 20 60.0
condition 6 12 50.0
subroutine 7 7 100.0
pod 2 2 100.0
total 77 95 81.0


line stmt bran cond sub pod time code
1             # BioPerl module for Bio::SeqIO::largefasta
2             #
3             # Please direct questions and support issues to
4             #
5             # Cared for by Jason Stajich
6             #
7             # Copyright Jason Stajich
8             #
9             # You may distribute this module under the same terms as perl itself
10             # _history
11             #
12             # POD documentation - main docs before the code
13              
14             =head1 NAME
15              
16             Bio::SeqIO::largefasta - method i/o on very large fasta sequence files
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 fasta flat
25             file databases.
26              
27             This module handles very large sequence files by using the
28             Bio::Seq::LargePrimarySeq module to store all the sequence data in
29             a file. This can be a problem if you have limited disk space on your
30             computer because this will effectively cause 2 copies of the sequence
31             file to reside on disk for the life of the
32             Bio::Seq::LargePrimarySeq object. The default location for this is
33             specified by the L-Etmpdir routine which is usually /tmp
34             on UNIX. If a sequence file is larger than the swap space (capacity
35             of the /tmp dir) this could cause problems for the machine. It is
36             possible to set the directory where the temporary file is located by
37             adding the following line to your code BEFORE calling next_seq. See
38             L for more information.
39              
40             $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir';
41              
42             =head1 FEEDBACK
43              
44             =head2 Mailing Lists
45              
46             User feedback is an integral part of the evolution of this and other
47             Bioperl modules. Send your comments and suggestions preferably to one
48             of the Bioperl mailing lists. Your participation is much appreciated.
49              
50             bioperl-l@bioperl.org - General discussion
51             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
52              
53             =head2 Support
54              
55             Please direct usage questions or support issues to the mailing list:
56              
57             I
58              
59             rather than to the module maintainer directly. Many experienced and
60             reponsive experts will be able look at the problem and quickly
61             address it. Please include a thorough description of the problem
62             with code and data examples if at all possible.
63              
64             =head2 Reporting Bugs
65              
66             Report bugs to the Bioperl bug tracking system to help us keep track
67             the bugs and their resolution. Bug reports can be submitted via the web:
68              
69             https://github.com/bioperl/bioperl-live/issues
70              
71             =head1 AUTHORS - Jason Stajich
72              
73             Email: jason@bioperl.org
74              
75             =head1 APPENDIX
76              
77             The rest of the documentation details each of the object
78             methods. Internal methods are usually preceded with a _
79              
80             =cut
81              
82             # Let the code begin...
83              
84             package Bio::SeqIO::largefasta;
85 1     1   444 use vars qw($FASTALINELEN);
  1         1  
  1         33  
86 1     1   4 use strict;
  1         1  
  1         14  
87              
88 1     1   236 use Bio::Seq::SeqFactory;
  1         2  
  1         31  
89              
90             $FASTALINELEN = 60;
91 1     1   4 use base qw(Bio::SeqIO);
  1         1  
  1         402  
92              
93             sub _initialize {
94 3     3   6 my($self,@args) = @_;
95 3         12 $self->SUPER::_initialize(@args);
96 3 50       10 if( ! defined $self->sequence_factory ) {
97 3         8 $self->sequence_factory(Bio::Seq::SeqFactory->new
98             (-verbose => $self->verbose(),
99             -type => 'Bio::Seq::LargePrimarySeq'));
100             }
101             }
102              
103             =head2 next_seq
104              
105             Title : next_seq
106             Usage : $seq = $stream->next_seq()
107             Function: returns the next sequence in the stream
108             Returns : A Bio::Seq::LargePrimarySeq object
109             Args : NONE
110              
111             =cut
112              
113             sub next_seq {
114 2     2 1 423 my ($self) = @_;
115             # local $/ = "\n";
116 2         6 my $largeseq = $self->sequence_factory->create();
117 2         3 my ($id,$fulldesc,$entry);
118 2         1 my $count = 0;
119 2         2 my $seen = 0;
120 2         14 while( defined ($entry = $self->_readline) ) {
121 5624 50 66     16271 if( $seen == 1 && $entry =~ /^\s*>/ ) {
122 0         0 $self->_pushback($entry);
123 0         0 return $largeseq;
124             }
125             # if ( ($entry eq '>') || eof($self->_fh) ) { $seen = 1; next; }
126 5624 50       8143 if ( ($entry eq '>') ) { $seen = 1; next; }
  0 100       0  
  0         0  
127             elsif( $entry =~ /\s*>(.+?)$/ ) {
128 2         4 $seen = 1;
129 2 50       15 ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/)
130             or $self->warn("Can't parse fasta header");
131 2         11 $largeseq->display_id($id);
132 2         7 $largeseq->primary_id($id);
133 2         6 $largeseq->desc($fulldesc);
134             } else {
135 5622         12758 $entry =~ s/\s+//g;
136 5622         7964 $largeseq->add_sequence_as_string($entry);
137             }
138 5624 50 66     12541 (++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n";
139             }
140 2 50       10 return unless $seen;
141 2         11 return $largeseq;
142             }
143              
144             =head2 write_seq
145              
146             Title : write_seq
147             Usage : $stream->write_seq(@seq)
148             Function: writes the $seq object into the stream
149             Returns : 1 for success and 0 for error
150             Args : Bio::Seq object
151              
152              
153             =cut
154              
155             sub write_seq {
156 1     1 1 341 my ($self,@seq) = @_;
157 1         2 foreach my $seq (@seq) {
158 1         7 my $top = $seq->id();
159 1 50 33     14 if ($seq->can('desc') and my $desc = $seq->desc()) {
160 1         2 $desc =~ s/\n//g;
161 1         3 $top .= " $desc";
162             }
163 1         6 $self->_print (">",$top,"\n");
164 1         2 my $end = $seq->length();
165 1         3 my $start = 1;
166 1         3 while( $start <= $end ) {
167 2811         2163 my $stop = $start + $FASTALINELEN - 1;
168 2811 100       3036 $stop = $end if( $stop > $end );
169 2811         3266 $self->_print($seq->subseq($start,$stop), "\n");
170 2811         3881 $start += $FASTALINELEN;
171             }
172             }
173              
174 1 50 33     8 $self->flush if $self->_flush_on_write && defined $self->_fh;
175 1         11 return 1;
176             }
177              
178             1;