organism.py - organism-specific functionality in cMonkey
 
This file is part of cMonkey Python. Please see README and LICENSE for
more information and licensing details.

Modules
		StringIO logging os cmonkey.patches re cmonkey.util

Classes
		RsatDatabase   class RsatDatabase     abstract interface to access an RSAT mirror     Methods defined here: __init__(self, base_url, cache_dir) create an RsatDatabase instance based on a mirror URL get_contig_sequence(self, organism, contig) returns the specified contig sequence get_feature_names(self, organism) returns the specified organism's feature name file contents get_features(self, organism) returns the specified organism's feature file contents Note: the current version only tries to read from feature.tab while the original cMonkey will fall back to cds.tab if that fails get_rsat_organism(self, kegg_organism) returns the HTML page for the directory listing get_taxonomy_id(self, organism) returns the specified organism name file contents Data and other attributes defined here: DIR_PATH = 'data/genomes' FEATURE_NAMES_PATH = 'genome/feature_names.tab' FEATURE_PATH = 'genome/feature.tab' ORGANISM_NAMES_PATH = 'genome/organism_names.tab' ORGANISM_PATH = 'genome/organism.tab'

Data
		__all__ = ['RsatDatabase']