Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file

SYNOPSIS

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See Bio::DB::Flat.

DESCRIPTION

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This module allows fasta files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

SEE ALSO

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Bio::DB::Flat,

AUTHOR - Lincoln Stein

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Email - lstein@cshl.org

BioPerl documentation Contained in the BioPerl distribution. 
#
#
# BioPerl module for Bio::DB::Flat::BDB
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Lincoln Stein <lstein@cshl.org>
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


package Bio::DB::Flat::BDB::fasta;

use strict;

use base qw(Bio::DB::Flat::BDB);

sub default_file_format { "fasta" }

sub seq_to_ids {
  my $self = shift;
  my $seq  = shift;
  my %ids;
  $ids{$self->primary_namespace} = $seq->primary_id;
  \%ids;
}

sub parse_one_record {
    my $self  = shift;
    my $fh    = shift;
    
    # fasta parses by changing $/ to '\n>', need to adjust accordingly
    my $adj = ( $^O =~ /mswin/i ) ? -2 : -1; 
    my $parser =
      $self->{cached_parsers}{fileno($fh)}
        ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
    my $seq = $parser->next_seq or return;
    $self->{flat_alphabet} ||= $seq->alphabet;
    my $ids = $self->seq_to_ids($seq);
    return ($ids, $adj);
}

1;