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Bio-GenBankParser-0.05
River stage zero No dependents
++
/ Bio::GenBankParser

NAME

Bio::GenBankParser - Parse::RecDescent parser for a GenBank record

VERSION

Version 0.05

SYNOPSIS

This module aims to improve on the BioPerl GenBank parser by using a grammar-based approach with Parse::RecDescent.

    use Bio::GenBankParser;

    my $parser = Bio::GenBankParser->new();

    local $/ = "//\n";
    while ( my $rec = <$input> ) {
        my $gb_rec = $parser->parse( $rec );
    }

Or:

    my $parser = Bio::GenBankParser->new( file => $file );
    while ( my $seq = $parser->next_seq ) {
        ...
    }

METHODS

new

  use Bio::GenBankParser;
  my $parser = Bio::GenBankParser->new;

file

    $parser->file('/path/to/file');

Informs the parser to read sequentially from a file.

current_record

    my $genbank_record = $parser->current_record;

Returns the current unparsed GenBank record.

next_seq

    my $seq = $parser->next_seq;

Returns the next sequence from the file.

parse

    my $rec = $parser->parse( $text );
    print $rec->{'ACCESSION'};

Parses a (single) GenBank record into a hash reference.

parser

Returns the Parse::RecDescent object.

grammar

Returns the Parse::RecDescent grammar for a GenBank record.

AUTHOR

Ken Youens-Clark <kclark at cpan.org>.

BUGS

Please report any bugs or feature requests to bug-bio-genbankparser at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-GenBankParser. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Bio::GenBankParser

ACKNOWLEDGEMENTS

Lincoln Stein, Doreen Ware and everyone at Cold Spring Harbor Lab.

COPYRIGHT & LICENSE

Copyright 2008 Ken Youens-Clark, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.