Haizhou Liu > Bio-KEGGI-v0.1.50 > Bio::KEGGI

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Module Version: v0.1.5   Source  

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
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