|
0
|
1 #
|
|
|
2 # $Id: GenBank.pm,v 1.10 2002/10/22 07:38:33 lapp Exp $
|
|
|
3 #
|
|
|
4 # BioPerl module for Bio::Index::Abstract
|
|
|
5 #
|
|
|
6 # Cared for by Ewan Birney <birney@sanger.ac.uk>
|
|
|
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::Index::GenBank - Interface for indexing (multiple) GenBank
|
|
|
15 .seq files (ie flat file GenBank format).
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 # Complete code for making an index for several
|
|
|
20 # GenBank files
|
|
|
21 use Bio::Index::GenBank;
|
|
|
22 use strict;
|
|
|
23
|
|
|
24 my $Index_File_Name = shift;
|
|
|
25 my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_Name,
|
|
|
26 '-write_flag' => 'WRITE');
|
|
|
27 $inx->make_index(@ARGV);
|
|
|
28
|
|
|
29 # Print out several sequences present in the index
|
|
|
30 # in gcg format
|
|
|
31 use Bio::Index::GenBank;
|
|
|
32 use Bio::SeqIO;
|
|
|
33 use strict;
|
|
|
34
|
|
|
35 my $Index_File_Name = shift;
|
|
|
36 my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_Name);
|
|
|
37 my $seqio = new Bio::SeqIO(-format => 'gcg');
|
|
|
38 foreach my $id (@ARGV) {
|
|
|
39 my $seq = $inx->fetch($id); # Returns Bio::Seq object
|
|
|
40 $seqio->write_seq($seq);
|
|
|
41 }
|
|
|
42
|
|
|
43 # alternatively
|
|
|
44
|
|
|
45 my $seq1 = $inx->get_Seq_by_id($id);
|
|
|
46 my $seq2 = $inx->get_Seq_by_acc($acc);
|
|
|
47
|
|
|
48 =head1 DESCRIPTION
|
|
|
49
|
|
|
50 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
|
|
|
51 and provides the basic funtionallity for indexing GenBank files, and
|
|
|
52 retrieving the sequence from them. Heavily snaffled from James Gilbert's
|
|
|
53 Fasta system. Note: for best results 'use strict'.
|
|
|
54
|
|
|
55 =head1 FEED_BACK
|
|
|
56
|
|
|
57 =head2 Mailing Lists
|
|
|
58
|
|
|
59 User feedback is an integral part of the evolution of this and other
|
|
|
60 Bioperl modules. Send your comments and suggestions preferably to one
|
|
|
61 of the Bioperl mailing lists. Your participation is much appreciated.
|
|
|
62
|
|
|
63 bioperl-l@bioperl.org - General discussion
|
|
|
64 http://bioperl.org/MailList.shtml - About the mailing lists
|
|
|
65
|
|
|
66 =head2 Reporting Bugs
|
|
|
67
|
|
|
68 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
69 the bugs and their resolution. Bug reports can be submitted via
|
|
|
70 email or the web:
|
|
|
71
|
|
|
72 bioperl-bugs@bio.perl.org
|
|
|
73 http://bugzilla.bioperl.org/
|
|
|
74
|
|
|
75 =head1 AUTHOR - Ewan Birney
|
|
|
76
|
|
|
77 Email - birney@ebi.ac.uk
|
|
|
78
|
|
|
79 =head1 APPENDIX
|
|
|
80
|
|
|
81 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
|
|
|
82
|
|
|
83 =cut
|
|
|
84
|
|
|
85
|
|
|
86 # Let's begin the code...
|
|
|
87
|
|
|
88
|
|
|
89 package Bio::Index::GenBank;
|
|
|
90
|
|
|
91 use vars qw($VERSION @ISA);
|
|
|
92 use strict;
|
|
|
93
|
|
|
94 use Bio::Index::AbstractSeq;
|
|
|
95 use Bio::Seq;
|
|
|
96
|
|
|
97 @ISA = qw(Bio::Index::AbstractSeq);
|
|
|
98
|
|
|
99 sub _type_stamp {
|
|
|
100 return '__GenBank_FLAT__'; # What kind of index are we?
|
|
|
101 }
|
|
|
102
|
|
|
103 #
|
|
|
104 # Suggested fix by Michael G Schwern <schwern@pobox.com> to
|
|
|
105 # get around a clash with CPAN shell...
|
|
|
106 #
|
|
|
107
|
|
|
108 BEGIN {
|
|
|
109 $VERSION = 0.1;
|
|
|
110 }
|
|
|
111
|
|
|
112 sub _version {
|
|
|
113 return $VERSION;
|
|
|
114 }
|
|
|
115
|
|
|
116 =head2 _index_file
|
|
|
117
|
|
|
118 Title : _index_file
|
|
|
119 Usage : $index->_index_file( $file_name, $i )
|
|
|
120 Function: Specialist function to index GenBank format files.
|
|
|
121 Is provided with a filename and an integer
|
|
|
122 by make_index in its SUPER class.
|
|
|
123 Example :
|
|
|
124 Returns :
|
|
|
125 Args :
|
|
|
126
|
|
|
127 =cut
|
|
|
128
|
|
|
129 sub _index_file {
|
|
|
130 my( $self,
|
|
|
131 $file, # File name
|
|
|
132 $i # Index-number of file being indexed
|
|
|
133 ) = @_;
|
|
|
134
|
|
|
135 my( $begin, # Offset from start of file of the start
|
|
|
136 # of the last found record.
|
|
|
137 $id, # ID of last found record.
|
|
|
138 @accs, # accession of last record. Also put into the index
|
|
|
139 );
|
|
|
140
|
|
|
141 $begin = 0;
|
|
|
142
|
|
|
143 open GenBank, $file or $self->throw("Can't open file for read : $file");
|
|
|
144
|
|
|
145 # Main indexing loop
|
|
|
146 $id = undef;
|
|
|
147 @accs = ();
|
|
|
148 while (<GenBank>) {
|
|
|
149 if( /^\/\// ) {
|
|
|
150 if( ! defined $id ) {
|
|
|
151 $self->throw("Got to a end of entry line for an GenBank flat file with no parsed ID. Considering this a problem!");
|
|
|
152 next;
|
|
|
153 }
|
|
|
154 if( ! @accs ) {
|
|
|
155 $self->warn("For id [$id] in GenBank flat file, got no accession number. Storing id index anyway");
|
|
|
156 }
|
|
|
157
|
|
|
158 $self->add_record($id, $i, $begin);
|
|
|
159
|
|
|
160 foreach my $acc (@accs) {
|
|
|
161 if( $acc ne $id ) {
|
|
|
162 $self->add_record($acc, $i, $begin);
|
|
|
163 }
|
|
|
164 }
|
|
|
165 @accs = ();
|
|
|
166 } elsif (/^LOCUS\s+(\S+)/) {
|
|
|
167 $id = $1;
|
|
|
168 # not sure if I like this. Assummes tell is in bytes.
|
|
|
169 # we could tell before each line and save it.
|
|
|
170 $begin = tell(GenBank) - length( $_ );
|
|
|
171
|
|
|
172 } elsif (/^ACCESSION(.*)/) { # ignore ? if there.
|
|
|
173 @accs = ($1 =~ /\s*(\S+)/g);
|
|
|
174 } elsif( /^VERSION(.*)/) {
|
|
|
175 my $a = $1;
|
|
|
176 $a =~ s/^\s+//;
|
|
|
177 $a =~ s/\s+$//;
|
|
|
178 $a =~ s/GI\://;
|
|
|
179 push @accs, split(/\s+/,$a);
|
|
|
180 } else {
|
|
|
181 # do nothing
|
|
|
182 }
|
|
|
183 }
|
|
|
184
|
|
|
185 close GenBank;
|
|
|
186 return 1;
|
|
|
187 }
|
|
|
188
|
|
|
189 =head2 _file_format
|
|
|
190
|
|
|
191 Title : _file_format
|
|
|
192 Usage : Internal function for indexing system
|
|
|
193 Function: Provides file format for this database
|
|
|
194 Example :
|
|
|
195 Returns :
|
|
|
196 Args :
|
|
|
197
|
|
|
198
|
|
|
199 =cut
|
|
|
200
|
|
|
201 sub _file_format{
|
|
|
202 my ($self,@args) = @_;
|
|
|
203
|
|
|
204 return 'GenBank';
|
|
|
205 }
|
|
|
206
|
|
|
207 1;
|
