1. HaploReg, RegulomeDB and more on Python programming
Lin Liu
Yang Li

3. HaploReg retrieves the ENCODE annotation for the selected SNP, as well as other SNPs in LD
Using the “Set Options” tab, the user can configure values such as the LD threshold and the population used from 1000 Genomes data used to calculate LD

4. RegulomeDB

9. Python programming wrap-up
if else
for and while loop
index: starts from 0, different from R
four important data structure:
list: a = [1, 2, 3, 4]; a.append(5)
tuple: a = (‘cat’, ‘dog’); a[0], a[1] = a[1], a[0]
dictionary: a = {‘chr1’:{10254:’G’, 13257:’T’}}; a.keys();
sets:
from sets import Set
species = Set([‘hs’, ‘mm’, ‘chimp’])
zoos = Set([‘mm’, ‘wolf’, ‘chimp’])
zoos | species
zoos & species
zoos - species

10. Some tricky fact: Shallow copy and deep copy List comprehension:
Shallow copy: a = [1,2,3]; b = a; b[2] = 4; print(a)
Deep copy:
from copy import deepcopy
a = [1, 2, 3]; b = deepcopy(a); b[2] = 4; print(a)
List comprehension:
Like in R: loops are slow slow slow
a = [1, 2, 3]; a = [b + 1 for b in a]; print(a)

11. How to read bam (binary) files in python?
import pybedtools
How to perform numerical computation in python?
import numpy as np
Include array and matrix calculation, very useful
How to use shell script in python?
Get all files in a folder
import os
os.listdir(“yourdirectory”)

12. Object oriented programming
Class and objects in python
class HMM:
#constructor
#transition_probs[i, j] is the probability of transitioning to state i from state j
#emission_probs[i, j] is the probability of emitting emission j while in state i
def __init__(self, transition_probs, emission_probs):
self._transition_probs = transition_probs
self._emission_probs = emission_probs
#accessors
def emission_dist(self, emission):
return self._emission_probs[:, emission]
@property
def num_states(self):
return self._transition_probs.shape[0]
def transition_probs(self):
return self._transition_probs

13. Interface with other programming language
Rpy: R and python interface
cygwin: python and C interface
When to use python?
Text manipulation
Some simple machine learning implementation (like using matlab)
Some very well-written package available: PyStan (Bayesian MCMC sampler), matlablib, pybedtools etc

14. When not to use python:
Large scale simulation: most often you cannot get rid of loops
Statistical analysis: R is much better and well curated
Best strategy: C interface python

15. Some good reference code for python
Check MACS14 python script
You can learn how to write a python script into an executable software from MACS14