###########################################################'
# 
# Client to download matrix-scan results from RSAT server.
#
#
# usage: matrix_scan_soap.py [-h] -s <SEQUENCE_FILE> -m <MATRIX_FILE> -u
#                             <P-VALUE>
# 
# 
# Required arguments:
#   -h, --help            show this help message and exit
#   -s <SEQUENCE_FILE>, --sequence_file <SEQUENCE_FILE>
#                         Sequence in FASTA format.
#   -m <MATRIX_FILE>, --matrix_file <MATRIX_FILE>
#                         Matrix in transfac format.
#   -u <P-VALUE>, --uth_pval <P-VALUE>
#                         Upper threshold for p-value.
# 
# Examples :
# 
# Print help
#  python matrix_scan_soap.py -h
#
# Run test files
#  python matrix_scan_soap.py -m param_matrix.txt -s param_sequence.txt -u 0.001
# 
# 
# Version 0.2 - 21/07/2014 - Celine HERNANDEZ, RSAT team
# 
###########################################################'

## Tested with python 2.7.3 and suds version 0.4.1
matrixscanClientVersion = '0.2 - 21/07/2014'


## Import required libraries
import logging
from suds.client import Client
import os, platform
import argparse

###########################################################'
## Define log options for suds

# Configure default log package to INFO
logging.basicConfig(level=logging.INFO)
# Configure log of suds clients to DEBUG for verbose output concerning Client request
logging.getLogger('suds.client').setLevel(logging.ERROR)


################################################################
## Define functions

def call_matrix_scan(service, args):
  """
  Send the request to the Web services.

  :param service: SOAP/WSDL services
  :param args: arguments
  """
  print("; Sending request to server\t" + server)
  result = rsat_service.matrix_scan(args)
  return result



  
###########################################################'
## Parameters for RSAT tool matrix-scan

## Read and process command-line

# Field to be filled
sequence_file = ''
matrix_file = ''
uth_pval = ''

# See https://docs.python.org/2/library/argparse.html

# Create the parser
parser = argparse.ArgumentParser(description='Client to download matrix-scan results from RSAT server.', epilog='Version '+matrixscanClientVersion)

# Define arguments
parser.add_argument('-i', '--sequence_file', metavar='<SEQUENCE_FILE>', 
                    type=argparse.FileType('r'), nargs=1, help='Sequence in FASTA format.', required=True)

parser.add_argument('-m', '--matrix_file', metavar='<MATRIX_FILE>', 
                    type=argparse.FileType('r'), nargs=1, help='Matrix in transfac format.', required=True)

parser.add_argument('-u', '--uth_pval', metavar='<P-VALUE>', 
                    type=float, nargs=1, help='Upper threshold for p-value.', required=True)

parser.add_argument('-s', '--server', metavar='<SERVER>', nargs=1, 
                    help='URL of an RSAT server (default: http://pedagogix-tagc.univ-mrs.fr/rsat).', 
                    required=False, default="http://pedagogix-tagc.univ-mrs.fr/rsat")

# Parse command line
args = parser.parse_args()

# Get values to be used (read files and format uth_pval)
sequence = args.sequence_file[0].read()
matrix = args.matrix_file[0].read()
uth = ['pval '+str(args.uth_pval[0])]
server = args.server[0]

###########################################################'
## Create the SOAP client to request the RSAT service

print("; Initializing the Web services client")

# Load Client class from suds
# Define URL for RSAT services 
wsdlUrl =  os.path.join(server + '/web_services/RSATWS.wsdl')
# Create the client
client = Client(wsdlUrl)
# Need service interface to perform requests
rsat_service = client.service

# Define client header (optional)
userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
    matrixscanClientVersion, 
    os.path.basename( __file__ ),
    platform.python_version(), 
    platform.system()
)
httpHeaders = {'User-agent': userAgent}
client.set_options(headers=httpHeaders)
client.set_options(timeout=300)

# Wrap all arguments into a named list (dictionary), including some hard-coded characters
arguments = {
	'sequence' : sequence, 
	'matrix' : matrix,
	'matrix_format' : 'transfac',
	'uth' : uth,
	'quick' : 1,
	'str' : 2,
	'origin' : 'start',
	'background_input' : 1, # this option requires 'markov'
	'markov' : 1,
	'pseudo' : 1,
	'n_treatment' : 'score',
	'background_pseudo' : 0.01,
	#'return_fields' : 'pval'
}

###########################################################'
## Perform SOAP request on RSAT server
result = call_matrix_scan(rsat_service, arguments)

###########################################################'
## Display request results
print('\n; Command performed on server')
print(result.command)
print('\n; Printing the result')
print(result.client)
print("; Job done")