1 / 15

HaploReg , RegulomeDB and more on Python programming

HaploReg , RegulomeDB and more on Python programming. Lin Liu Yang Li. HaploReg retrieves the ENCODE annotation for the selected SNP, as well as other SNPs in LD

gezana
Download Presentation

HaploReg , RegulomeDB and more on Python programming

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

  2. 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

  3. RegulomeDB

  4. 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

  5. Some tricky fact: • Shallow copy and deep copy • 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)

  6. 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”)

  7. 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 defemission_dist(self, emission): return self._emission_probs[:, emission] @property defnum_states(self): return self._transition_probs.shape[0] @property deftransition_probs(self): return self._transition_probs

  8. 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, pybedtoolsetc

  9. 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

  10. 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

More Related