Bio::KEGGI - Perl module to parse KEGG genome, ko and pathway files.
Version 0.1.5
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".
Bio::KEGGI is used to parse KEGG files:
ftp://ftp.genome.jp/pub/kegg/genes/genome
ftp://ftp.genome.jp/pub/kegg/genes/ko
ftp://ftp.genome.jp/pub/kegg/pathway/pathway
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>.
L<Bio::SeqIO::kegg> also provides a KEGG sequence input/output stream.
Haizhou Liu, zeroliu-at-gmail-dot-com
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.
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
To install Bio::KEGGI, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::KEGGI
CPAN shell
perl -MCPAN -e shell install Bio::KEGGI
For more information on module installation, please visit the detailed CPAN module installation guide.