NAME

Bio::KEGG::genome - Perl module to fetch details of KEGG file 'genome'.

DESCRIPTION

Fetch data from a Bio::KEGGI::genome object.

Some genomes contain multiple chromosomes or plasmids, these are designated
as genome 'components', which has 2 categories: 'chromosome' and 'plasmid'.

AUTHOR

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

VERSION

0.1.5

METHODS

abbrsp

Name:   abbrsp
Desc:   Get KEGG genome entry abbreciated species name.
Usage:  $sp = $o_kegg->abbrsp()
Args:
Return: A string

hamap_id

Name:   hamap_id
Desc:   Get KEGG genome entry HAMPA id.
Usage:  $hamap_id = $o_kegg->hamap_id()
Args:
Return: A string

anno

Name:   anno
Desc:   Get KEGG genome entry ANNOTATION information.
Usage:  $anno = $o_kegg->anno()
Args:
Return: A string

taxid

Name:   taxid
Desc:   Get KEGG genome entry taxonomy id.
Usage:  $taxid = $o_kegg->taxid()
Args:
Return: A string    

taxonomy

Name:   taxonomy
Desc:   Get KEGG genome entry taxonomy information.
usage:  $taxonomy = $o_kegg->taxonomy
Args:
Return: A string

data_src

Name:   data_src
Desc:   Get KEGG genome entry DATA_SOURCE information
Usage:  $data_src = $o_kegg->data_src()
Args:
Return: A string

comment

Name:   comment
Desc:   Get KEGG genome entry COMMENT.
usage:  $comment = $o_kegg->comment()
Args:
Return: A string

origin_db

Name:   origin_db
Desc:   Get KEGG genome entry ORIGINAL_DB.
usage:  $origin_db = $o_kegg->original_db()
Args:
Return: A string

component

Name:   component
Desc:   Get KEGG genome entry CHROMOSOME and PLASMID information.

$rh_component = [
    {
        'category'    => $category, # 'chromosome' or 'plasmid'
        'is_circular' => $is_cir,   # 0 or 1
        'name'        => $name,
        'refseq'      => $refseq_id,
        'length'      => $length
    },
    ...
]

Usage:  Bio::KEGG::genome->component()
Args:
Return: A reference to an array    

statistics

Name:   statistics
Disc:   Get KEGG genome entry STATISTICS information.
        
        $rh_statistics = {
            'nt'  => $nt,  # Number of nucleotides
            'prn' => $prn, # Number of protein genes
            'rna' => $rna, # Number of RNA genes 
        }

Usage:  $o_kegg->statistics()
Args:
Return: A reference to a hash.