import time

import argparse

import nonRedundantResolver

import overlapResolver

import gapFiller

import twoRepeatOneBridgeSolver

import houseKeeper

import IORobot

###################################################### Starting point

def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):

print "<3 Do cool things that matter <3"

# folderName = "S_cerivisea/"

# mummerLink = "MUMmer3.23/"

t0 = time.time()

parser = argparse.ArgumentParser(description='FinisherSC : a repeat-aware tool to upgrade de-novo assembly with long reads')

parser.add_argument('folderName')

parser.add_argument('mummerLink')

parser.add_argument('-p', '--pickup', help='Picks up existing work (input is noEmbed.fasta, improved.fasta or improved2.fasta)', required=False)

parser.add_argument('-o', '--mapcontigs', help='Maps new contigs to old contigs(input is of the format of contigs.fasta_improved3.fasta which means improved3.fasta will be mapped back to contigs.fasta; Output can be found in mappingResults.txt in the destinedFolder;)', required=False)

parser.add_argument('-f', '--fast', help= 'Fast aligns contigs (input is True)', required=False)

parser.add_argument('-par', '--parallel', help= 'Fast aligns contigs (input is maximum number of threads)', required=False)

parser.add_argument('-l', '--large', help= 'Large number of contigs/large size of contigs (input is True)', required=False)

args = vars(parser.parse_args())

print "args", args

pathExists, newFolderName, newMummerLink = houseKeeper.checkingPath(args['folderName'], args['mummerLink'])

if args['fast'] == "True":

houseKeeper.globalFast = True

else:

houseKeeper.globalFast = False

if args['parallel'] != None:

houseKeeper.globalParallel = int(args['parallel'])

else:

houseKeeper.globalParallel = 1

if args['large'] == "True":

houseKeeper.globalLarge = True

else:

houseKeeper.globalLarge = False

if pathExists:

mainFlow(newFolderName, newMummerLink, args['pickup'], args['mapcontigs'])

else:

print "Sorry. The above folders or files are missing. If you continue to have problems, please contact me(Ka-Kit Lam) at kklam@eecs.berkeley.edu"

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