File Coverage

Bio/DB/RefSeq.pm
Criterion Covered Total %
statement 12 28 42.8
branch 0 4 0.0
condition n/a
subroutine 4 6 66.6
pod 2 2 100.0
total 18 40 45.0


line stmt bran cond sub pod time code
1             #
2             #
3             # BioPerl module for Bio::DB::EMBL
4             #
5             # Please direct questions and support issues to
6             #
7             # Cared for by Heikki Lehvaslaiho
8             #
9             # Copyright Jason Stajich
10             #
11             # You may distribute this module under the same terms as perl itself
12              
13             # POD documentation - main docs before the code
14              
15             =head1 NAME
16              
17             Bio::DB::RefSeq - Database object interface for RefSeq retrieval
18              
19             =head1 SYNOPSIS
20              
21             use Bio::DB::RefSeq;
22              
23             $db = Bio::DB::RefSeq->new();
24              
25             # most of the time RefSeq_ID eq RefSeq acc
26             $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
27             print "accession is ", $seq->accession_number, "\n";
28              
29             # or changeing to accession number and Fasta format ...
30             $db->request_format('fasta');
31             $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
32             print "seq is ", $seq->seq, "\n";
33              
34             # especially when using versions, you better be prepared
35             # in not getting what what want
36             eval {
37             $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
38             };
39             print "accesion is ", $seq->accession_number, "\n" unless $@;
40              
41             # or ... best when downloading very large files, prevents
42             # keeping all of the file in memory
43              
44             # also don't want features, just sequence so let's save bandwith
45             # and request Fasta sequence
46             $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
47             -format => 'fasta');
48             my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
49             while( my $seq = $seqio->next_seq ) {
50             print "seqid is ", $seq->id, "\n";
51             }
52              
53             =head1 DESCRIPTION
54              
55             Allows the dynamic retrieval of sequence objects L from the
56             RefSeq database using the dbfetch script at EBI:
57              
58             http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
59              
60             In order to make changes transparent we have host type (currently only
61             ebi) and location (defaults to ebi) separated out. This allows later
62             additions of more servers in different geographical locations.
63              
64             The functionality of this module is inherited from L
65             which implements L.
66              
67             This module retrieves entries from EBI although it
68             retrives database entries produced at NCBI. When read into bioperl
69             objects, the parser for GenBank format it used. RefSeq is a
70             NONSTANDARD GenBank file so be ready for surprises.
71              
72             =head1 FEEDBACK
73              
74             =head2 Mailing Lists
75              
76             User feedback is an integral part of the evolution of this and other
77             Bioperl modules. Send your comments and suggestions preferably to one
78             of the Bioperl mailing lists. Your participation is much appreciated.
79              
80             bioperl-l@bioperl.org - General discussion
81             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
82              
83             =head2 Support
84              
85             Please direct usage questions or support issues to the mailing list:
86              
87             I
88              
89             rather than to the module maintainer directly. Many experienced and
90             reponsive experts will be able look at the problem and quickly
91             address it. Please include a thorough description of the problem
92             with code and data examples if at all possible.
93              
94             =head2 Reporting Bugs
95              
96             Report bugs to the Bioperl bug tracking system to help us keep track
97             the bugs and their resolution. Bug reports can be submitted via the
98             web:
99              
100             https://github.com/bioperl/bioperl-live/issues
101              
102             =head1 AUTHOR - Heikki Lehvaslaiho
103              
104             Email Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE
105              
106             =head1 APPENDIX
107              
108             The rest of the documentation details each of the object
109             methods. Internal methods are usually preceded with a _
110              
111             =cut
112              
113             # Let the code begin...
114              
115             package Bio::DB::RefSeq;
116 5     5   449 use strict;
  5         5  
  5         125  
117 5     5   14 use vars qw($MODVERSION %HOSTS %FORMATMAP $DEFAULTFORMAT);
  5         7  
  5         314  
118              
119             $MODVERSION = '0.1';
120              
121 5     5   16 use base qw(Bio::DB::DBFetch);
  5         5  
  5         1406  
122              
123             BEGIN {
124             # you can add your own here theoretically.
125 5     5   21 %HOSTS = (
126             'dbfetch' => {
127             baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=refseq&style=raw',
128             hosts => {
129             'ebi' => 'www.ebi.ac.uk'
130             }
131             }
132             );
133 5         15 %FORMATMAP = ( 'embl' => 'embl',
134             'genbank' => 'genbank',
135             'fasta' => 'fasta'
136             );
137 5         843 $DEFAULTFORMAT = 'genbank';
138             }
139              
140             sub new {
141 0     0 1   my ($class, @args ) = @_;
142 0           my $self = $class->SUPER::new(@args);
143              
144 0           $self->{ '_hosts' } = {};
145 0           $self->{ '_formatmap' } = {};
146              
147 0           $self->hosts(\%HOSTS);
148 0           $self->formatmap(\%FORMATMAP);
149 0           $self->{'_default_format'} = $DEFAULTFORMAT;
150              
151 0           return $self;
152             }
153              
154              
155             sub get_seq_stream {
156 0     0 1   my ($self,%qualifiers) = @_;
157 0 0         if( exists $qualifiers{'-uids'} ) {
158 0 0         if( ref($qualifiers{'-uids'}) =~ /ARRAY/i ) {
159 0           foreach my $u ( @{$qualifiers{'-uids'}} ) {
  0            
160 0           $u =~ s/^(\S+)\|//;
161             }
162             } else {
163 0           $qualifiers{'-uids'} =~ s/^(\S+)\|//;
164             }
165             }
166 0           $self->SUPER::get_seq_stream(%qualifiers);
167             }
168              
169             1;