NAME

Bio::KEGGI - Perl module to parse KEGG genome, ko and pathway files.

VERSION

Version 0.1.5

SYNOPSIS

use Bio::KEGGI;

my $keggi = Bio::KEGGI->new(
    -file => 'keggfilename',
    -type => 'filetype',
);

while (my $kegg = $keggi->next_rec) {
    print $kegg->id, "\n";
}

Now supported KEGG file type are "genome", "ko", "pathway" and "gene".

DESCRIPTION

Bio::KEGGI is used to parse KEGG files:

genome

ftp://ftp.genome.jp/pub/kegg/genes/genome

ko

ftp://ftp.genome.jp/pub/kegg/genes/ko

pathway

ftp://ftp.genome.jp/pub/kegg/pathway/pathway

gene

Organism gene entries. such as:

ftp://ftp.genome.jp/pub/kegg/genes/organisms/aac/A.acidocaldarius.ent

KEGG data details could be retrieved by module L<Bio::KEGG>.

SEE ALSO

L<Bio::SeqIO::kegg> also provides a KEGG sequence input/output stream.

AUTHOR

Haizhou Liu, zeroliu-at-gmail-dot-com

BUGS

This module works for Unix text file format only, which lines end with a
"\n".

Please use other softwares, such as dos2unix to convert input file if
necessary.

METHODS

new

    Name:   new
    Desc:   A constructor for a KEGGI object.
    Usage:  Bio::KEGGI->new(
                -file => $file,
		        -type => $type, # A fake parameter
            );
    Args:   $file: A KEGG file: genome, ko, pathway
            $type: 'genome', 'ko', 'pathway' or 'gene' 
    Return: A Bio::KEGGI object