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

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Module Version: v0.1.5   Source  

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.
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