GTseqTools/stats.py at main · stevemussmann/GTseqTools · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
from decimal import *

import math

class GTStats():
	'Class for calculating summary statistics'

	def __init__(self, l):
		self.l = l
		self.mean = 0.0
		self.stdev = 0.0
		self.med = 0.0
		self.mmin = 0.0
		self.mmax = 0.0

	def calcStats(self):
		if len(self.l)!=0:
			self.mean = self.calcMean(self.l)
			self.stdev = self.calcStdev(self.l, self.mean)
			self.med = self.calcMed(self.l)
			self.mmin = min(self.l)
			self.mmax = max(self.l)


	def calcMean(self,l):
		total = self.calcSum(l)
		mean = (total/len(l))
		return mean

	def calcSum(self, l):
		total = Decimal()
		for item in l:
			total+=item
		return total

	def calcStdev(self, l, mean):
		vals = list()
		for val in l:
			dev = (val-mean)**2
			vals.append(dev)
		total = self.calcSum(vals)
		if len(l)-1 == 0:
			return 0
		else:
			temp = total/Decimal((len(l)-1))
			stdev = Decimal(math.sqrt(temp))
			return stdev

	def calcMed(self,l):
		sl = sorted(l)
		llen = len(l)
		i = (llen-1) // 2

		if(llen % 2):
			return sl[i]
		else:
			return Decimal((sl[i] + sl[i+1])/Decimal(2))

	def printStats(self, fn, mode1, mode2):
		print("Proportion of missing data summary for " + mode1 + " " + mode2 + ".")
		print("Mean\tStDev\tMedian\tMin\tMax")

		fh = open(fn, 'a')
		fh.write(str(len(self.l)))
		fh.write(" ")
		fh.write(mode2)
		fh.write(" were ")
		fh.write(mode1)
		fh.write(" after applying missing data filters.\n")
		fh.write("Missing data stats for ")
		fh.write(mode1)
		fh.write(" ")
		fh.write(mode2)
		fh.write(":\n")
		fh.write("Mean\tStDev\tMedian\tMin\tMax\n")
		print(round(self.mean,3), "\t", round(self.stdev,3), "\t", round(self.med,3), "\t", round(self.mmin,3), "\t", round(self.mmax,3))
		print("")
		fh.write(str(round(self.mean,3)))
		fh.write("\t")
		fh.write(str(round(self.stdev,3)))
		fh.write("\t")
		fh.write(str(round(self.med,3)))
		fh.write("\t")
		fh.write(str(round(self.mmin,3)))
		fh.write("\t")
		fh.write(str(round(self.mmax,3)))
		fh.write("\n")
		fh.write("\n")

		fh.close()