SNPModule

In this module, there are two main functions designed specifically to calculate SNP statistics:

• Calculating MAF (Minor allele frequency) of a SNP
• Calculating HWE (Hardy Weinberg Equilibrium)

Files

• setup.py
• genstats.py
• README.md

Installing genstats

python setup.py install

Using the methods in genstats.py

After installation, to use the package in the python code, type:

from genestats import genstats
p = genstats()                    #initialise class variable
p.functionName(argument)          #function call  

Main functions

maf(dictionary)

calculate allele frequencies given genotype count, input is a dictionary with at least 2 genotypes, eg {'AA':10, 'AB':5}, key value must have length of 2 characters, such as AA, 00, 01, AB, et cetera. Return a tuple (minor allele, minor allele frequencies)

hwe(dictionary)

return chi-square value of hwe calculation of a SNP, input is a dictionary with 3 genotypes as keys and genotype counts as values, eg {'AA': 10, 'AB': 5, 'BB': 1}, key value must have length of 2 characters, such as AA, 00, 01, AB, et cetera.

Usable functions included in this module

sort_dict(dictionary) 

sort a dictionary, return tuple sorted by values by ascent

pop(item, list)

pop an item from a list

sq(n)

return n*n

sum(list)

return sum of all items in the list, item has to be numeric

mean(list)

return average values of all items in the list, item has to be numeric

median(list)

return median values of all items in the list, item has to be numeric

mod(list)

return mod values of all items in the list, item has to be numeric