#!/usr/bin/python

# vi: sw=4 ts=4 et:

"""cmonkey.py - cMonkey top-level module

This file is part of cMonkey Python. Please see README and LICENSE for

more information and licensing details.

"""

import os.path

import cmonkey.cmonkey_run as cmr

import cmonkey.datamatrix as dm

import cmonkey.util as util

import argparse

import logging

from cmonkey.schedule import make_schedule

import ConfigParser

import tempfile

import cmonkey.scoring as scoring

import random

def set_config(cmonkey_run, config):

raise Exception("no setting found to retrieve the MEME nmotifs function")

# if we were installed through Debian package management, default.ini is found here

SYSTEM_INI_PATH = '/etc/cmonkey-python/default.ini'

USER_INI_PATH = 'config/default.ini'

if __name__ == '__main__':

description = """cMonkey (Python port) (c) 2011-2012,

Institute for Systems Biology

This program is licensed under the General Public License V3.

See README and LICENSE for details.\n"""

# read default configuration parameters

config = ConfigParser.ConfigParser()

if os.path.exists(USER_INI_PATH):

config.read(USER_INI_PATH)

elif os.path.exists(SYSTEM_INI_PATH):

config.read(SYSTEM_INI_PATH)

else:

raise Exception('could not find default.ini !')

parser = argparse.ArgumentParser(description=description)

parser.add_argument('--ratios', required=True,

help='tab-separated ratios matrix file')

parser.add_argument('--organism', help='KEGG organism code', default=None)

parser.add_argument('--out', default=config.get("General", "output_dir"),

help='output directory')

parser.add_argument('--cachedir', default=config.get("General", "cache_dir"),

help="path to cache directory")

parser.add_argument('--string', help='tab-separated STRING file for the organism',

default=None)

parser.add_argument('--operons', help='tab-separated STRING file for the organism',

default=None)

parser.add_argument('--checkpoint', help='checkpoint-file')

parser.add_argument('--checkratios', action="store_true",

help='check gene expression quality')

parser.add_argument('--remap_network_nodes', action="store_true",

help='network nodes are not named to RSAT primary names')

parser.add_argument('--logfile', default=None, help="""path to log file""")

parser.add_argument('--keep_memeout', action="store_true",

help="""keep MEME output files""")

parser.add_argument('--ncbi_code', default=None, help="NCBI taxonomy id")

parser.add_argument('--numclusters', type=int,

default=None, help="override the number of clusters")

parser.add_argument('--nomotifs', action="store_true", help="deactivate motif scoring")

parser.add_argument('--nonetworks', action="store_true", help="deactivate network scoring")

parser.add_argument('--nostring', action="store_true", help="deactivate STRING network scoring")

parser.add_argument('--nooperons', action="store_true", help="deactivate operon network scoring")

parser.add_argument('--config', default=None, help="additional configuration file")

parser.add_argument('--debug', action="store_true",

help="""run in debug mode""")

parser.add_argument('--random_seed', type=int)

# RSAT overrides

parser.add_argument('--rsat_dir', default=None,

help="""RSAT override: data directory""")

parser.add_argument('--rsat_organism', default=None,

help="""override the RSAT organism name""")

args = parser.parse_args()

# no organism provided -> dummy organism

if args.organism is None:

print("WARNING - no organism provided - assuming that you want to score ratios only or don't use automatic download")

if not args.rsat_dir:

args.nomotifs = True

if not args.string and not args.operons:

args.nonetworks = True

# user overrides in config files

if args.config:

config.read(args.config)

matrix_factory = dm.DataMatrixFactory([dm.nochange_filter,

dm.center_scale_filter])

matrix_filename = args.ratios

if matrix_filename.startswith('http://'):

indata = util.read_url(matrix_filename)

infile = util.dfile_from_text(indata, has_header=True, quote='\"')

else:

infile = util.read_dfile(matrix_filename, has_header=True, quote='\"')

matrix = matrix_factory.create_from(infile)

infile = None

# override number of clusters either on the command line or through

# the config file

try:

num_clusters = config.getint("General", "num_clusters")

except:

num_clusters = args.numclusters

cmonkey_run = cmr.CMonkeyRun(args.organism, matrix,

string_file=args.string,

rsat_organism=args.rsat_organism,

log_filename=args.logfile,

remap_network_nodes=args.remap_network_nodes,

ncbi_code=args.ncbi_code,

num_clusters=num_clusters,

operon_file=args.operons,

rsat_dir=args.rsat_dir)

set_config(cmonkey_run, config)

cmonkey_run['output_dir'] = args.out

cmonkey_run['cache_dir'] = args.cachedir

cmonkey_run['debug'] = args.debug

cmonkey_run['keep_memeout'] = args.keep_memeout or args.debug

cmonkey_run['donetworks'] = not args.nonetworks

cmonkey_run['domotifs'] = not args.nomotifs and cmonkey_run['meme_version']

cmonkey_run['use_string'] = not args.nostring

cmonkey_run['use_operons'] = not args.nooperons

if args.random_seed:

cmonkey_run['random_seed'] = args.random_seed

if cmonkey_run['random_seed']:

random.seed(cmonkey_run['random_seed'])

util.r_set_seed(cmonkey_run['random_seed'])

proceed = True

checkratios = args.checkratios

if args.checkratios:

thesaurus = cmonkey_run.organism().thesaurus()

logging.info("Checking the quality of the input matrix names...")

found = [name for name in matrix.row_names if name in thesaurus]

num_found = len(found)

total = len(matrix.row_names)

percent = (float(num_found) / float(total)) * 100.0

proceed = percent > 50.0

# Set update frequency to every iteration, so the full results are written

if cmonkey_run['debug']:

cmonkey_run['stats_freq'] = 1

cmonkey_run['result_freq'] = 1

if not proceed:

logging.error("# genes found: %d, # total: %d, %f %% - please check your ratios file",

num_found, total, percent)

else:

if args.checkpoint:

cmonkey_run.run_from_checkpoint(args.checkpoint)

else:

cmonkey_run.run()