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1 #
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2 # $Id: embl.pm,v 1.4 2002/10/22 07:38:31 lapp Exp $
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3 #
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4 # BioPerl module for Bio::DB::Flat::BDB
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5 #
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6 # Cared for by Lincoln Stein <lstein@cshl.org>
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9
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10 # POD documentation - main docs before the code
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11
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12 =head1 NAME
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13
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14 Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file
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15
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16 =head1 SYNOPSIS
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17
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18 See Bio::DB::Flat.
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19
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20 =head1 DESCRIPTION
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21
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22 This module allows embl files to be stored in Berkeley DB flat files
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23 using the Open-Bio standard BDB-indexed flat file scheme. You should
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24 not be using this directly, but instead use it via Bio::DB::Flat.
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25
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26 =head1 FEEDBACK
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27
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28 =head2 Mailing Lists
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29
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30 User feedback is an integral part of the evolution of this and other
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31 Bioperl modules. Send your comments and suggestions preferably to one
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32 of the Bioperl mailing lists. Your participation is much appreciated.
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33
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34 bioperl-l@bioperl.org - General discussion
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35 http://bioperl.org/MailList.shtml - About the mailing lists
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36
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37 =head2 Reporting Bugs
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38
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39 Report bugs to the Bioperl bug tracking system to help us keep track
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40 the bugs and their resolution. Bug reports can be submitted via
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41 email or the web:
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42
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43 bioperl-bugs@bio.perl.org
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44 http://bugzilla.bioperl.org/
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45
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46 =head1 AUTHOR - Lincoln Stein
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47
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48 Email - lstein@cshl.org
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49
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50 =head1 SEE ALSO
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51
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52 L<Bio::DB::Flat>,
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53
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54 =cut
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55
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56 package Bio::DB::Flat::BDB::embl;
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57
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58 use strict;
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59 use Bio::DB::Flat::BDB;
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60 use vars '@ISA';
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61
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62 @ISA = qw(Bio::DB::Flat::BDB);
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63
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64 sub parse_one_record {
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65 my $self = shift;
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66 my $fh = shift;
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67 my $parser =
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68 $self->{embl_cached_parsers}{fileno($fh)} ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
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69 my $seq = $parser->next_seq;
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70 my $ids = $self->seq_to_ids($seq);
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71 return $ids;
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72 }
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73
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74 sub seq_to_ids {
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75 my $self = shift;
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76 my $seq = shift;
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77
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78 my $display_id = $seq->display_id;
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79 my $accession = $seq->accession_number;
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80 my %ids;
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81 $ids{ID} = $display_id;
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82 $ids{ACC} = $accession if defined $accession;
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83 return \%ids;
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84 }
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85
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86 sub default_primary_namespace {
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87 return "ID";
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88 }
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89
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90 sub default_secondary_namespaces {
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91 return qw(ACC);
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92 }
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93
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94 sub default_file_format { "embl" }
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95
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96
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97 1;
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