Python Assignment 1

Strings

Excercise 1

#!/usr/bin/env python
seq = raw_input("Enter a DNA sequence: ")
print "It is", len(seq), "bases long."

bases = ["adenine", "thymine", "cytosine", "guanine"]
print bases[0], seq.count('A')
print bases[1], seq.count('T')
print bases[2], seq.count('C')
print bases[3], seq.count('G')

Result: 

Enter a DNA sequence: ATTAC
It is 5 bases long.
adenine 2
thymine 2
cytosine 1
guanine 0

Exercise 2

#!/usr/bin/env python
seq = raw_input("Enter a DNA sequence: ")
seq = seq.upper()
print "It is", len(seq), "bases long."

bases = ["adenine", "thymine", "cytosine", "guanine"]
print bases[0], seq.count('A')
print bases[1], seq.count('T')
print bases[2], seq.count('C')
print bases[3], seq.count('G')

Result: 

Enter a DNA sequence: ATTgtc
It is 6 bases long.
adenine 1
thymine 3
cytosine 1
guanine 1

Exercise 3

#!/usr/bin/env python
seq = raw_input("Enter a DNA sequence: ")
seq = seq.upper()
print "It is", len(seq), "bases long."

bases = ["adenine", "thymine", "cytosine", "guanine"]
print bases[0], seq.count('A')
print bases[1], seq.count('T')
print bases[2], seq.count('C')
print bases[3], seq.count('G')
unknown = len(seq) - seq.count('A') - seq.count('T') - seq.count('C') - seq.count('G')
print "unknown", str(unknown)

Result: 

Enter a DNA sequence: ATTU*gtc
It is 8 bases long.
adenine 1
thymine 3
cytosine 1
guanine 1
unknown 2

'for' loop

Exercise 1

#!/usr/bin/env python
seq = raw_input("Enter a DNA sequence: ")
for i in range(10):
    print i, seq

Result: 

Enter a DNA sequence: TACG
0 TACG
1 TACG
2 TACG
3 TACG
4 TACG
5 TACG
6 TACG
7 TACG
8 TACG
9 TACG

Exercise 2

#!/usr/bin/env python
seq = raw_input("Enter a DNA sequence: ")
n = len(seq)
for i in range(n):
    print 'base', i, 'is', seq[i]

Result: 

Enter a DNA sequence: GTTCAG
base 0 is G
base 1 is T
base 2 is T
base 3 is C
base 4 is A
base 5 is G

Exercise 3

#!/usr/bin/env python
restriction_sites = [
        "GAATTC", # EcoRI
        "GGATCC", # BamHI
        "AAGCTT", # HindIII
]

for site in restriction_sites:
    print site

Result: 

GAATTC
GGATCC
AAGCTT

Exercise 4

#!/usr/bin/env python
site2name = {
    "GAATTC": "EcoRI",
    "GGATCC": "BamHI",
    "AAGCTT": "HindIII"
}

seq = raw_input("Enter your sequence: ")
for site in site2name.keys():
    if site in seq:
        print site2name[site], "(", site, ")", "is present"
    else:
        print site2name[site], "(", site, ")", "is not present"

Result: 

Enter your sequence: GAATTCTTTTT
EcoRI ( GAATTC ) is present
BamHI ( GGATCC ) is not present
HindIII ( AAGCTT ) is not present

'if' loop

Exercise 1

#!/usr/bin/env python
seq = raw_input("Enter your sequence: ")
bases = "ACGT"
for b in bases:
    if b in seq:
        print b, 'count:', seq.count(b)

Result: 

Enter your sequence: ACCAGGCA
A count: 3
C count: 3
G count: 2

Reading files

Exercise 1

#!/usr/bin/env python
fn = './10_sequences.seq'
f = open(fn,'r')
lines = f.readlines()
for i,l in enumerate(lines):
    print i+1, l.rstrip()

Result: 

1 CCTGTATTAGCAGCAGATTCGATTAGCTTTACAACAATTCAATAAAATAGCTTCGCGCTAA
2 ATTTTTAACTTTTCTCTGTCGTCGCACAATCGACTTTCTCTGTTTTCTTGGGTTTACCGGAA
3 TTGTTTCTGCTGCGATGAGGTATTGCTCGTCAGCCTGAGGCTGAAAATAAAATCCGTGGT
4 CACACCCAATAAGTTAGAGAGAGTACTTTGACTTGGAGCTGGAGGAATTTGACATAGTCGAT
5 TCTTCTCCAAGACGCATCCACGTGAACCGTTGTAACTATGTTCTGTGC
6 CCACACCAAAAAAACTTTCCACGTGAACCGAAAACGAAAGTCTTTGGTTTTAATCAATAA
7 GTGCTCTCTTCTCGGAGAGAGAAGGTGGGCTGCTTGTCTGCCGATGTACTTTATTAAATCCAATAA
8 CCACACCAAAAAAACTTTCCACGTGTGAACTATACTCCAAAAACGAAGTATTGGTTTATCATAA
9 TCTGAAAAGTGCAAAGAACGATGATGATGATGATAGAGGAACCTGAGCAGCCATGTCTGAACCTATAGC
10 GTATTGGTCGTCGTGCGACTAAATTAGGTAAAAAAGTAGTTCTAAGAGATTTTGATGATTCAATGCAAAGTTCTATTAATCGTTCAATTG

Exercise 2

#!/usr/bin/env python
f = open('./10_sequences.seq','r')
lines = f.readlines()
motif = 'CTATA'
for i,l in enumerate(lines):
    pos = l.find(motif)
    if pos != -1:
        print motif, 'is found in sequence', i+1, 'Position', pos, '(0 based)'
        print i+1, l.rstrip()

Result: 

CTATA is found in sequence 8 Position 29 (0 based)
8 CCACACCAAAAAAACTTTCCACGTGTGAACTATACTCCAAAAACGAAGTATTGGTTTATCATAA
CTATA is found in sequence 9 Position 62 (0 based)
9 TCTGAAAAGTGCAAAGAACGATGATGATGATGATAGAGGAACCTGAGCAGCCATGTCTGAACCTATAGC

Advanced exercises

Exercise 1: sum up, csv file

#!/usr/bin/env python
f = open('./numbers1.csv','r')
lines = f.readlines()
for l in lines:
    numbers = l.rstrip().split(',')
    numbers = [ int(i) for i in numbers ]
    row_sum = sum(numbers)
    print row_sum


Result: 

716
1139
11
1707
1516

Exercise 2: sum up

#!/usr/bin/env python
f = open('./numbers1.csv','r')
lines = f.readlines()
total = 0
for l in lines:
    numbers = l.rstrip().split(',')
    numbers = [ int(i) for i in numbers ]
    row_sum = sum(numbers)
    print row_sum
    total += row_sum
print 'Total:', total

Result: 

716
1139
11
1707
1516
Total: 5089

Exercise 3: sum up, csv file with quotes

#!/usr/bin/env python
f = open('./numbers2.csv','r')
lines = f.readlines()
total = 0
for l in lines:
    numbers = l.rstrip().split(',')
    numbers = [ i.strip() for i in numbers ] # remove space
    numbers = [ i.strip('"') for i in numbers ] # remove quotes
    numbers = [ int(i) for i in numbers ]
    row_sum = sum(numbers)
    print row_sum
    total += row_sum
print 'Total:', total

Result: 

716
1139
11
1707
1516
Total: 5089

Exercise 4: parse FASTA

#!/usr/bin/env python
f = open('./sample1.fa','r')
lines = f.readlines()
for l in lines:
    l = l.rstrip()
    if not l:
        print 'Header', h, 'refer to sequence', s
    elif l[0] == '>':
        h = l[1:]
        s = ''
    else:
        s += l

Result: 

Header YL069W-1.334 refer to sequence CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAA
Header YAL068C-7235.2170 refer to sequence TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCACAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGATACATTACGTGCAACCAAAAGTGTAAAATGATTGGTTGCAATGTTTCACCTAAATTACTT
Header YAL070W-223.3355 refer to sequence CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATCTAATATGCCT

Exercise 5: FASTA file with blank lines

#!/usr/bin/env python
f = open('./sample2.fa','r')
lines = f.readlines()
fasta = dict()
for l in lines:
    l = l.rstrip()
    if not l:
        next
    elif l[0] == '>':
        header = l[1:]
        fasta[header] = ''
    else:
        fasta[header] += l
for h,s in fasta.items():
    print 'Header', h, 'refer to sequence', s

Result: 

Header YAL070W-223.3355 refer to sequence CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATCTAATATGCCT
Header YL069W-1.334 refer to sequence CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAA
Header YAL068C-7235.2170 refer to sequence TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCACAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGATACATTACGTGCAACCAAAAGTGTAAAATGATTGGTTGCAATGTTTCACCTAAATTACTT
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