# vi: sw=4 ts=4 et:

Modules
		bz2 cPickle cmonkey.config cmonkey.debug gc gzip json logging cmonkey.membership cmonkey.meme cmonkey.microarray cmonkey.microbes_online cmonkey.motif numpy cmonkey.network cmonkey.organism os re cmonkey.rsat cmonkey.scoring cmonkey.sizes sqlite3 cmonkey.stringdb cmonkey.thesaurus cmonkey.util

Classes
		CMonkeyRun   class CMonkeyRun       Methods defined here: __getitem__(self, key) __init__(self, ratios, args) __setitem__(self, key, value) cleanup(self) cleanup this run object combined_rscores_pickle_path(self) make_organism(self) returns the organism object to work on membership(self) organism(self) returns the organism object to work on prepare_run(self, check_params=True) Setup output directories and scoring functions for the scoring. Separating setup and actual run facilitates testing report_params(self) residual_for(self, row_names, column_names) run(self) run_iteration(self, iteration) run_iterations(self) update_iteration(self, iteration) use_dummy_organism(self) check whether we use a dummy organism write_finish_info(self) write_mem_profile(self, outfile, iteration) write_memberships(self, conn, iteration) write_results(self, iteration_result) write iteration results to database write_start_info(self) write_stats(self, iteration_result)

Functions
		get_function_class(scorefun)

Data
		COG_WHOG_URL = 'ftp://ftp.ncbi.nih.gov/pub/COG/COG/whog' PIPELINE_SYSTEM_PATHS = {'default': '/etc/cmonkey-python/default_pipeline.json', 'rows': '/etc/cmonkey-python/rows_pipeline.json', 'rowsandmotifs': '/etc/cmonkey-python/rows_and_motifs_pipeline.json', 'rowsandnetworks': '/etc/cmonkey-python/rows_and_networks_pipeline.json'} PIPELINE_USER_PATHS = {'default': 'config/default_pipeline.json', 'rows': 'config/rows_pipeline.json', 'rowsandmotifs': 'config/rows_and_motifs_pipeline.json', 'rowsandnetworks': 'config/rows_and_networks_pipeline.json'} STRING_URL_PATTERN = 'http://networks.systemsbiology.net/string9/%s.gz' SYSTEM_GO_FILE_PATH = '/etc/cmonkey-python/proteome2taxid' SYSTEM_KEGG_FILE_PATH = '/etc/cmonkey-python/KEGG_taxonomy' USER_GO_FILE_PATH = 'config/proteome2taxid' USER_KEGG_FILE_PATH = 'config/KEGG_taxonomy' VERTEBRATES = set(['hsa', 'mmu', 'rno'])