#!/usr/bin/env python
import sys
import numpy as np
import os
from scipy.stats import mannwhitneyu,ranksums,ttest_ind,ks_2samp
def compare_by_position(bed1,bed2,xmfa):
pos_dict = {}
for i,bed in enumerate([bed1,bed2]):
pos_dict[i] = {}
with open(bed,'r') as fi:
for line in fi:
#2 1892198 1892199 TCMMTMTTMMM 0.5 - 16
csome,start,end,motif,perc_meth,strand,num_reads,probabilities = tuple(line.split('\t'))
pos_dict[i][(csome,start,end,strand)] = ((perc_meth,num_reads),np.asarray([float(p) for p in probabilities.strip().split(',')]))
for pos in pos_dict[0]:
if pos in pos_dict[1]:
try:
u,pval = mannwhitneyu(pos_dict[0][pos][1],pos_dict[0][pos][1],alternative='two-sided')
except ValueError:
u,pval = 'none','identical'
u2,pval2 = ranksums(pos_dict[0][pos][1],pos_dict[0][pos][1])
try:
t,pval3 = ttest_ind(pos_dict[0][pos][1],pos_dict[0][pos][1])
except:
t,pval3 = 'none','missing df'
d,pval4 = ks_2samp(pos_dict[0][pos][1],pos_dict[0][pos][1])
if pval4 < 0.9:
print pos, pos_dict[0][pos][0], pos_dict[1][pos][0], pval, pval2, pval3, pval4
def main():
#parse command line options
from argparse import ArgumentParser
parser = ArgumentParser(description='Compare methylation between two genomes by probabilities of methylation for aligned positions')
parser.add_argument('--bed1',type=str,required=True,help='bed file 1 with verbose output from make_bed.py')
parser.add_argument('--bed2',type=str,required=True,help='bed file 2 with verbose output from make_bed.py')
parser.add_argument('-g','--genome_alignment',type=str,required=False,help='an xmfa file from mauve (if absent, alignments assumed to be to the same reference genome)')
parser.add_argument('-v','--version',action='store_true',required=False,help='print version')
args = parser.parse_args()
if args.version:
print 'mCallerNP 0.1'
sys.exit(0)
assert os.path.isfile(args.bed1), 'file not found at '+args.bed1
assert os.path.isfile(args.bed2), 'file not found at '+args.bed2
compare_by_position(args.bed1,args.bed2,args.genome_alignment)
if __name__ == "__main__":
main()
