UNIVERSITY OF ENGINEERING AND TECHNOLOGY LAHORE, NAROWAL CAMPUS

Assignment #2

Submitted to:
Mam Fatima Shahzadi

Submitted by:
Muhammad Ijaz Ahmad

Registration No#:
2023-BME-143

Course Name:
Introduction to computer programming for Data Science

Course Code:
CS-103

Department of Biomedical Engineering

Code is:
import numpy as np
import matplotlib.pyplot as plt
import random
# Function to generate a random DNA sequence
def generate_random_dna_sequence(length):
nucleotides = ['A', 'T', 'C', 'G']
return ''.join(random.choices(nucleotides, k=length))
# Function to generate a DNA profile in FASTA format for an individual
def generate_dna_profile(name, sequence):
fasta_format = f">{name}\n{sequence}\n"
return fasta_format
# Number of individuals and length of DNA sequence
num_individuals = 50
sequence_length = 100
# Generate DNA profiles for different individuals
dna_profiles = {}
for i in range(num_individuals):
name = f"Individual_{i+1}"
sequence = generate_random_dna_sequence(sequence_length)
dna_profiles[name] = sequence
# Write DNA profiles to a FASTA file
fasta_file = "dna_profiles.fasta"
with open(fasta_file, 'w') as file:
for name, sequence in dna_profiles.items():
file.write(generate_dna_profile(name, sequence))
print("DNA profiles have been generated and saved in 'dna_profiles.fasta'.")
# Data Loading and Preprocessing
dna_profiles_loaded = {}
with open(fasta_file, 'r') as file:
 lines = file.readlines()
for i in range(0, len(lines), 2):
name = lines[i].strip()[1:]
sequence = lines[i+1].strip()
dna_profiles_loaded[name] = sequence
# Encode DNA sequences into numerical arrays
alphabet = ['A', 'T', 'C', 'G']
encoded_profiles = np.array([[alphabet.index(base) for base in sequence] for sequence in
dna_profiles_loaded.values()])
# Generate DNA sample for crime scene simulation
crime_scene_sample = generate_random_dna_sequence(sequence_length)
# Encode the crime scene sample into a numerical array
encoded_crime_scene_sample = np.array([alphabet.index(base) for base in crime_scene_sample])
# Sequence Comparison
similarity_scores = [np.sum(encoded_crime_scene_sample == profile) for profile in encoded_profiles]
# Plot the result on a histogram
plt.figure(figsize=(10, 6))
plt.hist(similarity_scores, bins=np.arange(sequence_length+1), color='skyblue', edgecolor='black')
plt.xlabel('Similarity Score')
plt.ylabel('Frequency')
plt.title('DNA Profile Similarity to Crime Scene Sample')
plt.show()

Output is:
>Individual_1

ATACAGGTCCCGTCAGAGAGTTCGCAATGCATCACATGAGAAACGTGGATTCGCATTCTGGCCATAAGATGGGGA
TACGCGAGAGATCACCCCGAATGAA

>Individual_2

CAACATGTAAGTGCAACTGGACCTGAGCGAGAAGTCGGTAGATCTGACAACCCAATCAGTCGTGCCCCAGACTCA
CAAACCCTAGGCCAGGCGGCGGTGA

>Individual_3

AAATACGCGCTGGTATTGCTTGGTATAGGCTTTGCGAGGACTCAAAGTTTTTTCGAGAGTTGCGGAGCATCCGCTT
GGTGCTCAATCGTAATACTTTTCC
>Individual_4

GAGTTAGACCACCGAGGTATCTCTGATACGTGAGAGATCTTAAACCGCGTTCCTGGGGGGTGACAGACTTCAGAG
ACTAGTAAGCAGACGCAGTCCGCGG

>Individual_5

ACCCGATGGAGTCGCGGGGCGGCCCCGGCGCACTGCGGCGGCTCCAAAGAGCCCCGGTCAGGGCAATGATTGACC
ATAGACTGGGTGCGTGGTACGTTCC

>Individual_6

CGGATACACGCCATACCTCAGTAAAAAGTTATGGCGATAAAATAAAGTGTACCCCTTTCCATCTTGTTACTCGCAA
GTTCCTTGAGGGAAAAAATACACT

>Individual_7

TGCCTCGCCCGCTATGCTAATAAGATTTGGCCCCCACAAGCTCATGTCTATCGTGAGGAACATCATCTGTTAGGAC
CGCACGCAAGAGGATATCCAAGAT

>Individual_8

CTCGTGATTTTATTAGTCTTATCCACTCAGGCTTTTGAGTATTTATTTAGGGTACCACGCGCTGCAGAGTTATTCCTG
AATCTAGCACGGTTTCAAGGAG

>Individual_9

CTTGCTCCAATAACATGTTGGCAACTAAATGAACCCGGAAAGCGCTTCTTGGCAGGGAGGGATTAAGGACTAACA
GCCTACATGATCCGAAACGGTTAAG

>Individual_10

GGTCTCGTCAGTTGACCGCCATCAACCCGGGTACTTAACACTTTCCGCGAACACTATGCACTGATCAATTGACCCA
TCTAGAGTGTACCAGATTTGAAAT

>Individual_11

CTGTTTTGTCGAACAAGAACAGTATAGGGCACCAACGAAGGCGACCAAGGGCGGCGGCCCTTCACGTATACACCC
AAGCACCGGAAGTTTAGTTCAGGGA

>Individual_12

AATACTGCCAGTCGGCTGGTTCGCGTTCTATAATTCTAAGACATGATAACCCACGAGAGGTTTTAACGGGCGTGGG
AACATCCAGGTATCGGACCCCTGG

>Individual_13

CCGCTTTCCGACGGAAGATCTAAAGTAAAACCCCTTCGATTCATGATGCTGATCCAAGCTACAAACTGACGTCACA
GCCGCTAGGGGAGGACTAACGGTT

>Individual_14

CATCCGTAACGCGTGGAACCGCAATGGTATTTTAGGGCGTTTAGCTAAATAGCAATTATGGCTGCGTACAATCAGT
TGTGCCGATAGTTCCAATGGCGTG

>Individual_15

TTTCGAGATACGTACCGAAATCGACGCTCTATTGCGTTTCAGTATGTGCCCTGTTCTGGGAAGCTATATCGACTAAA
TGTAGCGACATAAGATGTAACCG

>Individual_16

TTTTAACGGGGGAAGTACTCACCCGGACTTAGGATGCGATACAGGGGGGGATTCATGTTTCTAACCATGAGCGGTC
ACGTGTTGGACTGAGGGTAGGCCC
>Individual_17

GTACTGAGGCAATGGCCGCGTCCCCGTGCTCGACAGTTGAGCAGCAACATGCGTTTGAATCTGTGAAACATCTTGT
TTACGATACTGTTACTTATACCTA

>Individual_18

CGTTGACCTTTTCAGGATCCGTTCACGCTGGGTTTTAACGTGCGCGCTTTATAATGTGGAAGGCGGGGGGGAGTCC
CACACGAGCTATTTACTCCAACCT

>Individual_19

GGAGCGTCACGTCTATAGCTTATGTCCTACTGGGGTCGGCCCATGAAAGAGGAGTATCTATGCGTTCTATGGTAGA
TTCCACGCTAAGACTCGGCCATCA

>Individual_20

GCGTTCCTGTTTCTCCCCTCGACTGGGTAATGGAGCCGACCTGCGAGCTCACGTTATCTTAAAATGAGCTGGTTCCC
AGTACTAAGTCCGGCCGACGTGT

>Individual_21

CCACTGCAAGCAGTTCAAATGCTACCGTGGGAATCGGCACATTTTAGGAGAACTTTTGTGACATTTCGAGACTGTC
AAGCACCCACTGCAAATCAATTAT

>Individual_22

ATAAGTTTACGGAGCAATAGCGTCTACAAAAAATTCAATTGTGCAGGCCCGGTGAACCTCTAGTCGTACATGAACG
CAACGGGTATTGAAGCCGCAAGAT

>Individual_23

TCGATTCGCTATGCCCCATCCACCTCGCAAATAGTCGCGTCCTCGTATACTTACCTTAGACTACACGGAGGTCTAAC
CGTTACGACGTAGGCAATTCGTG

>Individual_24

CGCCCCTCGCTGTGTTTGTCAATAGGTAATTTTTTGAGAACCAACGGCCTTATACTATCTCGGCTATCACACGGTAG
AAGTGGAACTCACACCAGGAGTC

>Individual_25

TGACAGCTCCCCAGAAGAGACACCAGATGTCTATCTAAGTTGTTTAGTCTGTGCTAGTTCTACCAGTAAACATGAT
TGAAAAAACTATCTTATTCTTCTG

>Individual_26

TAATTTGCTGCGCGCGTGCCCCTCTACGTCGGATAAGTAATCAGATGGTACTCCAAGCGTAAATCACTTCTCCATTT
CTACCTTGGGGTCTGATATAGTC

>Individual_27

ATATGAATCAGCTGTTCTGGCTTGTAGTAACGAGGGGCCATATGGAAAGTATCCTGCCAAACGGCAGGTAGAAAT
CACAGCGTCCGAGCTTACCATGGTT

>Individual_28

TAGTTCAGACGGAAGGGGGGAAACTCCAAGGGTCCGCAAGTCCAAAATGAGCACGCATGCCCAACTATACTGCAC
ATAAACTCATGTTTCGCGCGTTCGC

>Individual_29

AACAGACGTTTGCTAAAAGTGCATAAAGTCGGACCGCGCTGATTTAGTACGCAGGCCGGAATGAGACATAACAGG
ACTACAAGACTCTACAACCCGAGAT
>Individual_30

CAGTTTCAATAAGATAAGGCCAGTCTAATGGAGAATGAATCTGCAACTCCCTAAAGAAGTGGTGGCGCACGTCCG
TGGAGGCCAGCGCCCTAGAGATATC

>Individual_31

TTCTCCCCTAGCAGTAAATTCTTCAGACACCAGCTGGTACCTTAGTGAAGTAAAAGTGAACTTTCATTTGGTTACAG
CCCGGCAAGGATATACGGCTGAG

>Individual_32

AACTATATAGGAAGTCTCAGCCACCACAAAAGTTACGGGCAGCGGGGGTGCTCCGTCAAGTCCGAGAAGGCGAAT
AGCGCTGATAATTTATGTCACACTC

>Individual_33

AGGGAGGAAGTCCGAGAAAACAGTAATAAATACCTCGGGCGTAATAGATAAAGTACAAGCAATTGTCGTTAGTCA
ATCGATTGCGTGGTGGAGACTGCCG

>Individual_34

AGCTGGCCGGGCATGCGTTGCGTGGCCAAGCTTAGTACTCATGTAGCCGACGGAGCCTCATCAAACTGAGCGTCA
ATTAGTTGGAGGGTTGTAGTTAATA

>Individual_35

AGGTAGAGCTCACACAGGTATAAAGTGCTCAGTCAAAGGCAGGCCATAATCGCGGACGATTAATACCCATATCCA
TGCGAGTCCGTGGAGAGATCGTACA

>Individual_36

CAAATCTATGGGCCACCTAGCATAGCACACTGAAGAACGCGCATAAAGGTAGATACTAAGCGTTTATGGGATGTT
TTCGGGTTAGCGGCTAACTCATAAA

>Individual_37

GACTTCGAGCAAGACGCACTTAATCGATAATTGCCGCCTGTTTGGGTGCTCGATACATTGGGTCACACGCCTCCAT
GGGGAGTCGTGAGCGAAGGTCTGG

>Individual_38

CCCGATATTGGTTTTAAGCTCCACCCTTCACACGAGGTGCTAGAACCGTAGAGTTCCCTCGTATAGAGCTTTAAGT
GATTGAGATTAGGTGGAGGATTCC

>Individual_39

TTGGCTATCTGGACTTTATCTAAGTCTGAACGCTATCTAGATTGTATTTGCGCGGATTGAATGCAATCTCCGAATAG
ATGGCGCAGTGGGCAAAATACCC

>Individual_40

AGTACCCAAAATGTACGCCGACCACACCAGAAAAGTTTAGACTTGTTATCAGATACTTCGCAGGATTGGTGGGAC
GACACTCGCACGTTGTAATTTCTCT

>Individual_41

ATCTGATCATATTTTTGACTGTGAACGTATATACGTCCAGTCGCTTGGTTTATATTCTCCACGTCGCTTTGGCTCCAC
AGGCCGACTCGTAGTTCGGTGT

>Individual_42

CTTGGTTGTGGTCCGCCAAGGACATCTCACGCTCCAAGAGATGGGACTGGCCAATAGGCGCAGACAAAACTTCTC
CACCTCCAGCTTAAGGCAGGATCTT
>Individual_43

GGTACCAAGTTATCGTGTGTGTTCGCTAGGAAATTAGTTTTTAGTCATCGACAGGATTGCGTCCTACACTATTATGA
AAACAAGTCATAGGGCATAGCAC

>Individual_44

GATCCACCAATACTACCCATAGTATCAGTCCAACGCTCTCCCACAACGCGGGCTTGGGGGCACTTACGAGAGGGG
GTGGAACTAGGGGCTATCCTCGAAA

>Individual_45

TCCGCTGATAAATAACGACGTCAAGAAAAGCTCTGAAATATCCCTAAGTATTAATATGTTTTTGAGCTCTACGGCC
ATCAGTCACCCTACTAGCGTAGTC

>Individual_46

CTTCCCAAAAACAAACCTGTAAAGGCTCTTTCCGCTATAAGCGGATCTTCTTAAGAATTGTTCAGTCGCGCTTCACC
ATCTGCTGTGTATTACCAAAGTC

>Individual_47

TCTATACAATAACTGTGGCGTAGCAATACACTGACAAGCGGCTTTTTATGTAGCGGTCGGGCTTCCCTACTCAGAT
TGCCAGTAAATTACGGTCGTCTGT

>Individual_48

CTTGCATTCGCGCTTGTATGCTCTCTGTACTGATGAGAAAGGTCCCATCCTAGTGGCGCGGTACGTGTTTTCAGCCG
AAAAGGCCGTAACGTGGGGACGA

>Individual_49

TAGAGGCCCAGCAAACGTACTCCCTGTAGGTTACTGACGGACTCGCGTATGGCGATGCTTTGTAGGCATATTCCGT
AATCTTGATTAGAGTTGGTAAATA

>Individual_50

CAGAACATGAAACGGCGGCCAGAGAACGTACGGTCGCTTAGCAGACGCCCAGTTGGATTGTCGTAGAAACAGACG
CGCGATGTCCTTAGCCACAGGTTAC

Graph is: