Bio/DB/Flat/BDB/fasta.pm

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