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HaploReg, RegulomeDB and more on Python programming

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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

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