Bio::KEGG::genome - Perl module to fetch details of KEGG file 'genome'.
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'.
Haizhou Liu, zeroliu-at-gmail-dot-com
0.1.5
Name: abbrsp Desc: Get KEGG genome entry abbreciated species name. Usage: $sp = $o_kegg->abbrsp() Args: Return: A string
Name: hamap_id Desc: Get KEGG genome entry HAMPA id. Usage: $hamap_id = $o_kegg->hamap_id() Args: Return: A string
Name: anno Desc: Get KEGG genome entry ANNOTATION information. Usage: $anno = $o_kegg->anno() Args: Return: A string
Name: taxid Desc: Get KEGG genome entry taxonomy id. Usage: $taxid = $o_kegg->taxid() Args: Return: A string
Name: taxonomy Desc: Get KEGG genome entry taxonomy information. usage: $taxonomy = $o_kegg->taxonomy Args: Return: A string
Name: data_src Desc: Get KEGG genome entry DATA_SOURCE information Usage: $data_src = $o_kegg->data_src() Args: Return: A string
Name: comment Desc: Get KEGG genome entry COMMENT. usage: $comment = $o_kegg->comment() Args: Return: A string
Name: origin_db Desc: Get KEGG genome entry ORIGINAL_DB. usage: $origin_db = $o_kegg->original_db() Args: Return: A string
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
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.
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.