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diffMeth4.py
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diffMeth4.py
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#!/usr/bin/python
# JMG 4/26/16
# Testing regions for differential methylation.
# Performs pairwise comparisons for all groups of
# samples, reports difference in average
# methylation and p-value based on Welch's
# t-test (two-tailed).
import sys
import gzip
scip = 0 # boolean for scipy import
try:
from scipy import stats
except ImportError:
sys.stderr.write('Warning! The scipy module is not installed\n'
+ ' (see www.scipy.org/install.html).\n'
+ ' All p-values will be reported as "NA".\n')
scip = 1
def usage():
print '''Usage: python diffMeth4.py [options] -i <input> -o <output> \\
<groupList1> <groupList2> [...]
<groupList> Comma-separated list of sample names (as found in
the header of <input>)
<input> File listing genomic regions and methylation results
(output from combineRegions2.py)
Options (whether or not to report a region):
-c <int> Minimum number of CpGs in a region (def. 1)
-d <float> Minimum methylation difference between sample groups
([0-1]; def. 0 [all results reported])
-p <float> Maximum p-value ([0-1]; def. 1 [all results reported])
-up Report only regions hypermethylated in later group
-down Report only regions hypomethylated in later group
-dna Report regions whose diff is 'NA' (occurs when one
group has no methylation data)
-pna Report regions whose p-value is 'NA' (occurs when one
group does not have multiple data points)'''
sys.exit(-1)
def openRead(filename):
'''
Open filename for reading. '-' indicates stdin.
'.gz' suffix indicates gzip compression.
'''
if filename == '-':
return sys.stdin
try:
if filename[-3:] == '.gz':
f = gzip.open(filename, 'rb')
else:
f = open(filename, 'rU')
except IOError:
sys.stderr.write('Error! Cannot open %s for reading\n' % filename)
sys.exit(-1)
return f
def openWrite(filename):
'''
Open filename for writing. '-' indicates stdout.
'.gz' suffix indicates gzip compression.
'''
if filename == '-':
return sys.stdout
try:
if filename[-3:] == '.gz':
f = gzip.open(filename, 'wb')
else:
f = open(filename, 'w')
except IOError:
sys.stderr.write('Error! Cannot open %s for writing\n' % filename)
sys.exit(-1)
return f
def getInt(arg):
'''
Convert given argument to int.
'''
try:
val = int(arg)
except ValueError:
sys.stderr.write('Error! Cannot convert %s to int\n' % arg)
sys.exit(-1)
return val
def getFloat(arg, minVal = None, maxVal = None):
'''
Convert given argument to float. Ensure it is within a
supplied range, if applicable.
'''
try:
val = float(arg)
except ValueError:
sys.stderr.write('Error! Cannot convert %s to float\n' % arg)
sys.exit(-1)
if (minVal != None and val < minVal) or \
(maxVal != None and val > maxVal):
sys.stderr.write('Error! Value %f is outside of range [%f,%f]\n' \
% (val, minVal, maxVal))
sys.exit(-1)
return val
def getSample(csv):
'''
Return a list of samples.
'''
arr = []
for tok in csv.split(','):
arr.append(tok)
return arr
def saveIndexes(fIn, samples):
'''
Find indexes for samples in header of input file.
Also save indexes for extra fields:
'gene', 'distance', 'location'
'''
idxs = [] # for indexes
res = [] # for ordered sample names
for i in range(len(samples)):
idxs.append([])
res.append([])
# extra fields to keep
extra = ['gene', 'distance', 'location']
idxExtra = []
resExtra = []
# get indexes
header = fIn.readline().rstrip()
spl = header.split('\t')
for i in range(len(spl)):
for j in range(len(samples)):
if spl[i] in samples[j]:
idxs[j].append(i)
res[j].append(spl[i])
if spl[i] in extra:
idxExtra.append(i)
resExtra.append(spl[i])
# make sure all samples were found
for i in range(len(idxs)):
if len(idxs[i]) != len(samples[i]):
sys.stderr.write('Error! Cannot find all sample names' \
+ ' in input file\n')
sys.exit(-1)
# construct header for output file
head = spl[:4]
for i in range(len(res)):
head += [','.join(res[i])]
head += resExtra
for i in range(len(res)-1):
for j in range(i+1, len(res)):
base = ','.join(res[i]) + '->' + ','.join(res[j])
head += [base + '_diff', base + '_pval']
return idxs, idxExtra, head
def calcDiff(avg1, avg2, meth1, meth2):
'''
Calculate methylation difference and p-value for
two samples.
'''
if avg1 == 'NA' or avg2 == 'NA':
return 'NA', 'NA'
# calculate methylation difference
diff = avg2 - avg1
# calculate p-value (Welch's t-test)
if len(meth1) < 2 or len(meth2) < 2 or scip:
pval = 'NA'
elif diff == 0:
pval = 1
elif max(meth1) - min(meth1) == 0 and \
max(meth2) - min(meth2) == 0:
pval = 0
else:
pval = stats.ttest_ind(meth1, meth2, equal_var=False)[1]
return diff, pval
def calcAvg(spl, idxs):
'''
Calculate average for a subset of values in a list.
'''
avg = 0.0
vals = [] # for saving numerical values
for idx in idxs:
if spl[idx] == 'NA':
continue
val = getFloat(spl[idx])
avg += val
vals.append(val)
if vals:
avg /= len(vals)
return avg, vals
def isPrintable(diff, pval, minDiff, maxPval, up, down, dna, pna):
'''
Determine if result should be printed, based
on diff, pval, and CL parameters.
'''
if diff == 'NA':
if not dna: return 0
elif (up and diff <= 0) or (down and diff >= 0) or \
abs(diff) < minDiff: return 0
if pval == 'NA':
if not pna: return 0
elif pval > maxPval: return 0
return 1
def processLine(line, idxs, idxExtra, minCpG, minDiff, maxPval,
up, down, dna, pna):
'''
Process a line containing methylation data for a set of samples.
'''
spl = line.split('\t')
if len(spl) < max([max(idx) for idx in idxs]):
sys.stderr.write('Error! Poorly formatted record:\n%s' % line)
return []
if getInt(spl[3]) < minCpG:
return [] # fewer than min. CpGs
# calculate averages
avg = [] # for average methylation fractions
meth = [] # for methylation values
data = 0 # valid methylation data boolean
for idx in idxs:
val, vals = calcAvg(spl, idx)
if vals:
avg.append(val)
meth.append(vals)
data = 1
else:
avg.append('NA')
meth.append('NA')
if not data:
return []
# calculate differences and p-values for each possible
# combination of two samples
ans = [] # for saving diffs and p-vals
pr = 0 # boolean for printing line
for i in range(len(avg)-1):
for j in range(i+1, len(avg)):
diff, pval = calcDiff(avg[i], avg[j], meth[i], meth[j])
ans.extend((diff, pval))
# determine if result should be printed
if pr == 0:
pr = isPrintable(diff, pval, minDiff, maxPval, \
up, down, dna, pna)
# return if no (significant) diffs for any group comparisons
if not pr:
return []
# construct record for output file
res = spl[:4] # chrom, pos, CpGs
for val in avg:
res.append(str(val)) # avg. methylation fraction
for idx in idxExtra:
res.append(spl[idx]) # extra fields
for val in ans:
res.append(str(val)) # diffs and p-values
return res
def main():
'''
Main.
'''
# Default parameters
minCpG = 0 # min. number of CpGs
minDiff = 0 # min. methylation difference
maxPval = 1 # max. p-value
up = 0 # report only hypermethylated (boolean)
down = 0 # report only hypomethylated (boolean)
dna = 0 # report results with diff of 'NA'
pna = 0 # report results with pval of 'NA'
if scip:
pna = 1 # if no scipy, all pvals are 'NA'
# get command-line args
args = sys.argv[1:]
if len(args) < 2: usage()
fIn = None
fOut = None
samples = []
i = 0
while i < len(args):
if args[i] == '-i':
fIn = openRead(args[i+1])
elif args[i] == '-o':
fOut = openWrite(args[i+1])
elif args[i] == '-c':
minCpG = getInt(args[i+1])
elif args[i] == '-d':
minDiff = getFloat(args[i+1], 0, 1)
elif args[i] == '-p':
maxPval = getFloat(args[i+1], 0, 1)
elif args[i] == '-up':
up = 1
elif args[i] == '-down':
down = 1
elif args[i] == '-dna':
dna = 1
elif args[i] == '-pna':
pna = 1
elif args[i] == '-h':
usage()
else:
samples.append(getSample(args[i]))
if args[i][0] == '-' and len(args[i]) == 2:
i += 2
else:
i += 1
# check for errors
if fIn == None or fOut == None:
sys.stderr.write('Error! Must specify input and output files\n')
usage()
if len(samples) < 2:
sys.stderr.write('Error! Must have at least two sets of samples\n')
usage()
# save indexes of samples from header
idxs, idxExtra, res = saveIndexes(fIn, samples)
fOut.write('\t'.join(res) + '\n')
# process file
count = 0
for line in fIn:
res = processLine(line.rstrip(), idxs, idxExtra, \
minCpG, minDiff, maxPval, up, down, dna, pna)
if res:
fOut.write('\t'.join(res) + '\n')
count += 1
sys.stderr.write('Regions printed: %d\n' % count)
fIn.close()
fOut.close()
if __name__ == '__main__':
main()