'''

Typical usage :

python postme.py \

-o datafolder/ \

-a ~/Desktop/allinone/experimentBench/MUMmer3.23/ \

-c mFixed2.fasta \

-r LR.fasta

'''

### Standard librariess

import argparse

import json

import time

import os

### Local libraries

import alignmentLib

import cTestLib

import graphLib

import houseKeeperLib

import rankingLib

import readConnectivityLib

import setCoverLib

def mainFlow(folderName, mummerLink, inputContigsFilename, inputReadsFilename, useSpades, noAlignment, scoreListOutputName, outputContigsFilename, mScoreThres, conScoreThres, setCoverOption):

rankingLib.rankAndMerge(folderName,contigsNamesList, contigsFilename, readsFilename, scoreListWithDummy, contigGapReadLookUpDic, mScoreThres, conScoreThres, scoreListOutputName, outputContigsFilename, dummyNodeDataRobot)

parser = argparse.ArgumentParser(description='PostMe')

parser.add_argument('-o', '--outputFolder', help= 'Output folder path', required=False)

parser.add_argument('-a', '--alignmentPath', help= 'MUMmer path', required=False)

parser.add_argument('-r', '--readsFilename', help= 'Filename for reads file', required=False)

parser.add_argument('-c', '--contigsFilename', help= 'Filename for contigs file', required=False)

parser.add_argument('-s', '--inputCoverageViaSpadesHeader', help= 'Input coverage from spades header files (T/F)', required=False)

parser.add_argument('-na', '--noAlignment', help= 'Use existing alignment file (T/F)', required=False)

parser.add_argument('-sn', '--scoreListOutputName', help= 'Output filename for scoreList', required=False)

parser.add_argument('-on', '--outputContigsFilename', help= 'Output filename for the improved contigs in FASTA format', required=False)

parser.add_argument('-ms', '--mScoreCutOff', help= 'Number of spanning reads cutoff', required=False)

parser.add_argument('-cs', '--cScoreCutOff', help= 'Abundance confidence score cutoff', required=False)

parser.add_argument('-co', '--setCoverOption', help= 'Set cover algorithms to be used', required=False)

args = vars(parser.parse_args())

folderName, mummerLink = houseKeeperLib.trailingFolderCorrection(args['outputFolder']) , houseKeeperLib.trailingFolderCorrection(args['alignmentPath'])

contigsFilename, readsFilename = args['contigsFilename'], args['readsFilename']

useSpades = True if args['inputCoverageViaSpadesHeader'] == 'T' else False

noAlignment = True if args['noAlignment'] == 'T' else False

scoreListOutputName = args['scoreListOutputName'] if args['scoreListOutputName'] != None else "scoreList.json"

outputContigsFilename = args['outputContigsFilename'] if args['outputContigsFilename'] != None else "improved.fasta"

mScoreThres = int(args['mScoreCutOff']) if args['mScoreCutOff'] != None else 2

conScoreThres = float(args['cScoreCutOff']) if args['cScoreCutOff'] != None else 0.95

setCoverOption = 'greedy' if args['setCoverOption'] == 'greedy' else 'baseline'

t0 = time.time()

mainFlow(folderName, mummerLink, contigsFilename, readsFilename, useSpades, noAlignment, scoreListOutputName, outputContigsFilename, mScoreThres, conScoreThres, setCoverOption)

print "Time", time.time() - t0