Bio::GenBankParser - Parse::RecDescent parser for a GenBank record
Version 0.05
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 ) {
...
}
use Bio::GenBankParser;
my $parser = Bio::GenBankParser->new;
$parser->file('/path/to/file');
Informs the parser to read sequentially from a file.
my $genbank_record = $parser->current_record;
Returns the current unparsed GenBank record.
my $seq = $parser->next_seq;
Returns the next sequence from the file.
my $rec = $parser->parse( $text );
print $rec->{'ACCESSION'};
Parses a (single) GenBank record into a hash reference.
Returns the Parse::RecDescent object.
Returns the Parse::RecDescent grammar for a GenBank record.
Ken Youens-Clark .
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.
You can find documentation for this module with the perldoc command.
perldoc Bio::GenBankParser
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Lincoln Stein, Doreen Ware and everyone at Cold Spring Harbor Lab.
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.