Lecture 2, Introduction to Python. Python Programming Language

Lecture 2, Introduction to Python

Young-Rae Cho

Associate Professor

Department of Computer Science

Baylor University

BINF 3360, Introduction to Computational Biology

Python Programming Language

Script Language

 General-purpose script language

 Broad applications

(web, bioinformatics, network programming, graphics, software engineering)

Features

 Object-oriented

 Extension with modules

 Database integration

 Embeddable

Getting Started

Download & Installation

 http://www.python.org/download/ (the most recent version: Python 3.3)

Edit & Run

 Create a file named test.py

 Edit the code

 Run the code

# This is a test. dna = ‘ATCGATGA’ print dna, ‘\n’

> python test.py

Primitives

Primitive Data Types

 Numbers or Strings

Substring

Reversing

num = 1234 st = ‘1234’

num_1 = num + int(st) st_1 = str(num) + st dna1 = ‘ACGTGAACT’ dna2 = dna1[::-1] dna1 = ‘ACGTGAACT’ dna2 = dna1[0:4] length = len(dna2)

Lists

List Variables

 A list of comma-separated values

 Insert, Delete, Append, Reverse, and Sort lst1 = [‘A’, ‘C’, ‘G’] lst2 = [‘T’] lst1 = lst1 + lst2 Variable-length list lst = [‘A’, ‘T’, ‘G’] lst.insert(1, ‘C’) del lst[2] lst.append(‘T’) lst.extend([‘A’, ‘C’]) lst.reverse() lst.sort() lst = [‘A’, ‘T’, ‘G’] lst [1:2] = ‘C’ lst [1:1] = ‘T’ lst [2:3] = ‘’ lst [len(lst) : len(lst)] = ‘T’ lst [len(lst) : len(lst)] = [‘A’, ‘C’] lst [::-1]

Sets

Set Variables

Add and Remove

DNAbases = {‘A’, ‘C’, ‘G’, ‘T’} RNAbases = {‘A’, ‘C’, ‘G’, ‘U’} DNAbases | RNAbases DNAbases & RNAbases DNAbases - RNAbases

bases = {‘A’, ‘D’, ‘G’} bases.add(‘T’) bases.remove(‘D’)

Dictionaries

Initialization Mapping Delete d = dict() d[‘key1’] = ‘value1’ k2, v2 = ‘key2’, ‘value2’ d[k2] = v2 d = { ‘key1’: ‘value1’ , ‘key2’: ‘value2’ , ‘key3’: ‘value3’ } d[‘key1’] d.get(‘key1’) d.keys() d.values() del d[‘key1’]

Input / Output

Standard Input Reading Files  Writing Files name = ‘myfilename.txt’ with open(name) as file:

data = file.read()

name = sys.stdin.readline() with open(name) as file:

data = file.read()

name = sys.argv[1] with open(name) as file:

data = file.read() import sys

data = sys.stdin.readline().replace(‘\n’, ‘ ’)

name = ‘output.txt’ with open(name, ‘w’) as file:

Functions

 Types

 Built-in system functions

 User-defined functions

 Defining Function

 Function Call

def function_name (parameter_list): statement statement return value

Iteration

Iterative Process def find_max(lst): max_so_far = lst[0] for item in lst[1:]: if item > max_so_far: max_so_far = item return max_so_far lst1 = [3,5,10,4,6] maximum = find_max(lst1)

Recursion

Recursive Call

def print_tree(tree, level): print ‘ ’ * 4 * level, tree[0] for subtree in tree[1:]:

print_tree(subtree, level+1) t1 = [‘A’, [‘T’, [‘A’], [‘T’]], [‘G’, [‘G’], [‘C’]]] print_tree(t1, 0)

Modules

Module  A collection of functions

 Module python (.py) files in a library directory

Module Call

import random seq = 'ATCGATAGCTA'

random_base = seq[random.randint(0,len(seq)-1)]

from random import * seq = 'ATCGATAGCTA'

Regular Expressions

Special Languages  Metacharacters  Quantifiers  Alternatives  Character Set Usage

Same to the regular expressions in Perl

import re

if re.match(‘TATA .* AA’, seq): print ‘It matched!’

import re

matches = re.findall(‘TATA .* AA’, seq) print matches

Biological Applications

Parsing Sequences

Base Frequency Counting

Motif (Substring) Search

Sequence Transformation

 DNA Replication

 Transcription from DNA to RNA

 Translating RNA into Protein

Parsing Sequences (1)

Single Sequence in FASTA Format

Parsing

 Make a function to return the sequence from the FASTA format >gi|5524211|gb|AAD44166.1| cytochrome b LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIP YIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDK IPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRS VPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYP YTIIGQMASILYFSIILAFLPIAGXIENY def read_FASTA_seq(filename): with open(filename) as f: return f.read().partition(‘\n’)[2].replace(‘\n’, ‘’)

Parsing Sequences (2)

Multiple Sequences in FASTA Format

Parsing ? >SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIP QFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFY VMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQIATIGE NLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

Frequency Counting

DNA Sequence Validation

Counting Base Frquency

 Make a function to calculate the percent of ‘C’ and ‘G’ in a DNA sequence

def validate_dna (base_sequence): seq = base_sequence.upper() return len(seq) == (seq.count(‘T’) +

seq.count(‘C’) + seq.count(‘A’) + seq.count(‘G’) )

def validate_dna (base_sequence): seq = base_sequence.upper() for base in seq:

if base not in ‘ACGT’: return False return True

def percent_of_GC (base_sequence): seq = base_sequence.upper()

return (seq.count(‘G’) + seq.count(‘C’)) / len(seq)

Motif Search

Searching Substring

 Make a function to take a sequence and a motif and return the position(s) of matching in the sequence

def motif_search (seq, motif): return seq.find(motif)

def all_motif_search (seq, motif): pos = []

idx = seq.find(motif) pos.append(idx)

seq = seq.partition(motif)[2] while seq.find(motif) >= 0:

idx += seq.find(motif) + len(motif) pos.append(idx)

Transcription

Simulating Transcription

 Make a function to transcribe a DNA into an RNA

def transcription (dna): return dna.replace(‘T’, ‘U’)

Translation (1)

Making Genetic Code

 Make a function to translate a codon to an amino acid

def codon2aa(codon):

genetic_code = { ‘UUU’: ‘F’, ‘UUC’: ‘F’, ‘UUA’: ‘L’, …… } if codon in genetic_code.keys():

return genetic_code[codon] else:

Translation (2)

Simulating Translation

 Make a function to translate an RNA into a protein sequence

def translation(rna): protein = ‘’

for n in range(0, len(rna), 3): protein += codon2aa(rna[n:n+3]) return protein

Translation (3)

Simulating Translation – cont’

 Make a generator

- an object that returns values from a series it computes

def aa_generator(rna):

return (codon2aa(rna[n:n+3]) for n in range(0, len(rna), 3) )

def translation(rna): gen = aa_generator(rna) protein = ‘’

aa = next(gen) while aa:

Mutation

Simulating Mutation

 Make a function to simulate single point mutations in a DNA sequence

import random def mutation(dna): position = random.randint(0,len(dna)-1) bases = ‘ACGT’ new_base = bases[random.randint(0,3)] dna[position:position+1] = new_base return dna bases.replace(dna[position], ‘’) new_base = bases[random.randint(0,2)]

Questions?

 Lecture Slides are found on the Course Website, web.ecs.baylor.edu/faculty/cho/3360