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makeSumMaster.py
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#!/usr/bin/env python
sampleFile = raw_input("sample file path: ")
parameters = raw_input("parameters, i.e. mq20, mq20_mc3, mq30: ")
outfileName = raw_input("outfile name: ")
def make_geneList():
geneList = []
with open("/home/mrood/scripts/importantFiles/genes_ordered.txt", 'r') as infile:
for line in infile:
gene = line.strip()
geneList.append(gene)
return geneList
def make_geneDict():
geneDict = {}
with open("/home/mrood/scripts/importantFiles/PerGeneSummary.txt", 'r') as infile:
for line in infile:
line = line.strip().split('\t')
geneDict[line[0]] = [line[1], line[3], line[7]]
#print geneDict["Rv0001"] #test to make sure generated
return geneDict
def make_sampleList(sampleFile):
samples = []
with open(sampleFile, 'r') as infile:
for line in infile:
line = line.strip()
samples.append(line)
print('There are {0} samples to be processed.'.format(len(samples)))
return samples
def make_dicts(geneList, samples):
d = {}
stats = ["theta", "pi", "TD", "piNpiS"]
for sample in samples:
d[sample] = {}
for stat in stats:
d[sample][stat] = {}
for gene in geneList:
d[sample]["theta"][gene] = ["-", "-"]
d[sample]["pi"][gene] = "-"
d[sample]["TD"][gene] = "-"
d[sample]["piNpiS"][gene] = ["-","-","-"]
d["global"] = {}
for stat in stats:
d["global"][stat] = {}
for gene in geneList:
d["global"]["theta"][gene] = ["-", "-", "-"]
d["global"]["pi"][gene] = "-"
d["global"]["TD"][gene] = "-"
d["global"]["piNpiS"][gene] = ["-","-","-","-","-","-","-"]
return d
def pop_dg(d):
with open("global/global.genes.tajD", 'r') as file:
for line in file:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[2])
except ValueError:
cov = line[2]
if type(cov) == float and cov >= 0.55:
d["global"]["TD"][gene] = line[3]
with open("global/global.genes.pi", 'r') as file:
for line in file:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[2])
except ValueError:
cov = line[2]
if type(cov) == float and cov >= 0.55:
d["global"]["pi"][gene] = line[3]
passGenes = []
with open("global/global.genes.theta", 'r') as file:
for line in file:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[2])
except ValueError:
cov = line[2]
if type(cov) == float and cov >= 0.55:
d["global"]["theta"][gene] = line[1:]
passGenes.append(gene)
print("global sample has " + str(len(passGenes)) + " genes with >= 0.55 coverage")
with open("global/global_syn-nonsyn.pi", 'r') as infile:
for line in infile:
line = line.strip().split('\t')
gene = line[0]
if gene in passGenes:
if float(line[5]) == 0:
if float(line[6]) == 0:
NS = "NaN"
else:
NS = "DQ"
elif float(line[6]) == 0:
NS = "Inf"
else:
NS = float(line[5])/float(line[6])
d["global"]["piNpiS"][gene] = [line[1],line[2],line[3],line[4],line[5],line[6],str(NS)]
return d
def pop_di(d, samples):
for sample in samples:
with open('tajD/' + sample + '_' + parameters + '_tajD.genes.mean', 'r') as file:
next(file)
for line in file:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[1])
except ValueError:
cov = line[1]
if type(cov) == float and cov >= 0.55:
d[sample]["TD"][gene] = line[12]
with open('pi/' + sample + '_' + parameters + '_pi.genes.mean', 'r') as infile:
next(infile)
for line in infile:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[1])
except ValueError:
cov = line[1]
if type(cov) == float and cov >= 0.55:
d[sample]["pi"][gene] = line[12]
passGenes = []
with open("theta/" + sample + '_' + parameters + '_theta.genes.mean', 'r') as infile3:
for line in infile3:
line = line.strip().split('\t')
gene = line[0]
try:
cov = float(line[1])
except ValueError:
cov = line[1]
if type(cov) == float and cov >= 0.55:
d[sample]["theta"][gene] = [line[1],line[12]]
passGenes.append(gene)
print(sample + " has " + str(len(passGenes)) + " genes with >= 0.55 coverage")
#with open('piNpiS/' + sample + '_med.calc', 'r') as infile4:
# next(infile4)
# for line in infile4:
# line = line.strip().split('\t')
# gene = line[0]
# if gene in passGenes:
# d[sample]["piNpiS"][gene] = [line[1],line[3],line[5]]
with open('piNpiS/' + sample + '_' + parameters + '_med.calc', 'r') as infile4:
next(infile4)
for line in infile4:
line = line.strip().split('\t')
gene = line[0]
if gene in passGenes and line[1] != "NA":
if float(line[1]) == 0:
if float(line[2]) == 0:
NS = "NaN"
else:
NS = "DQ"
elif float(line[2]) == 0:
NS = "Inf"
else:
NS = float(line[1])/float(line[2])
d[sample]["piNpiS"][gene] = [line[1],line[2],str(NS)]
return d
def write_files(geneList, geneDict, d, samples):
with open(outfileName, 'w') as outfile:
outfile.write(
'gene.symbol\tgene.name\tgene.length\tgene.des\tg.snps\tg.coverage\tg.theta\tg.pi\tg.TD\tg.NSlen\tg.Slen\tg.NSsnps\tg.Ssnps\tg.piN\tg.piS\tg.piN.piS')
for sample in samples:
outfile.write("\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %
(sample+'.cov',
sample+'.theta',
sample+'.pi',
sample+'.tajD',
sample+'.piN',
sample+'.piS',
sample+'.piNpiS'))
outfile.write('\n')
for gene in geneList:
try:
outfile.write(gene + '\t' + "\t".join(geneDict[gene]) + '\t')
except KeyError:
print('KeyError: ' + gene)
outfile.write(gene + '\t\t\t')
allSamps = ["global"] + samples
for sample in allSamps:
outfile.write("%s\t%s\t%s\t%s\t" %
("\t".join(d[sample]["theta"][gene]),
d[sample]["pi"][gene],
d[sample]["TD"][gene],
"\t".join(d[sample]["piNpiS"][gene])
))
outfile.write('\n')
geneList = make_geneList()
geneDict = make_geneDict()
samples = make_sampleList(sampleFile)
d = make_dicts(geneList, samples)
dg = pop_dg(d)
dgi = pop_di(dg, samples)
write_files(geneList, geneDict, dgi, samples)