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.
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 <kclark at cpan.org>.
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.
bug-bio-genbankparser at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Bio::GenBankParser
RT: CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-GenBankParser
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-GenBankParser
CPAN Ratings
http://cpanratings.perl.org/d/Bio-GenBankParser
Search CPAN
http://search.cpan.org/dist/Bio-GenBankParser
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.
To install Bio::GenBankParser, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::GenBankParser
CPAN shell
perl -MCPAN -e shell install Bio::GenBankParser
For more information on module installation, please visit the detailed CPAN module installation guide.