Bio/DB/Flat/BDB/fasta.pm

   1 #
   2 # $Id$
   3 #
   4 # BioPerl module for Bio::DB::Flat::BDB
   5 #
   6 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   7 #
   8 # Cared for by Lincoln Stein <lstein@cshl.org>
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file
  17
  18 =head1 SYNOPSIS
  19
  20 See Bio::DB::Flat.
  21
  22 =head1 DESCRIPTION
  23
  24 This module allows fasta files to be stored in Berkeley DB flat files
  25 using the Open-Bio standard BDB-indexed flat file scheme.  You should
  26 not be using this directly, but instead use it via Bio::DB::Flat.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to one
  34 of the Bioperl mailing lists.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 the bugs and their resolution.  Bug reports can be submitted via the
  54 web:
  55
  56   http://bugzilla.open-bio.org/
  57
  58 =head1 SEE ALSO
  59
  60 L<Bio::DB::Flat>,
  61
  62 =head1 AUTHOR - Lincoln Stein
  63
  64 Email - lstein@cshl.org
  65
  66 =cut
  67
  68 package Bio::DB::Flat::BDB::fasta;
  69
  70 use strict;
  71
  72 use base qw(Bio::DB::Flat::BDB);
  73
  74 sub default_file_format { "fasta" }
  75
  76 sub seq_to_ids {
  77   my $self = shift;
  78   my $seq  = shift;
  79   my %ids;
  80   $ids{$self->primary_namespace} = $seq->primary_id;
  81   \%ids;
  82 }
  83
  84 sub parse_one_record {
  85     my $self  = shift;
  86     my $fh    = shift;
  87
  88     # fasta parses by changing $/ to '\n>', need to adjust accordingly
  89     my $adj = ( $^O =~ /mswin/i ) ? -2 : -1;
  90     my $parser =
  91       $self->{cached_parsers}{fileno($fh)}
  92         ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
  93     my $seq = $parser->next_seq or return;
  94     $self->{flat_alphabet} ||= $seq->alphabet;
  95     my $ids = $self->seq_to_ids($seq);
  96     return ($ids, $adj);
  97 }
  98
  99 1;