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p2 Python Project

This program asks the user to enter a number of DNA sequences. It then finds the consensus sequence by analyzing the sequences column by column to determine the nucleotide frequencies and the maximum nucleotide repetitions in each column. It outputs the consensus sequence and displays the nucleotide frequencies in each column for each sequence.

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Daniella Vargas
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30 views3 pages

p2 Python Project

This program asks the user to enter a number of DNA sequences. It then finds the consensus sequence by analyzing the sequences column by column to determine the nucleotide frequencies and the maximum nucleotide repetitions in each column. It outputs the consensus sequence and displays the nucleotide frequencies in each column for each sequence.

Uploaded by

Daniella Vargas
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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"""This program ask the user to enter a number of DNA sequences and finds the

consensus sequence. The ouput is the consensus.


Add the corresponding code to accomplish the requested tasks
"""

##### ADD YOUR NAME, Student ID, and Section number #######
# NAME: Daniella Vargas Figueroa
# STUDENT ID:802228453
# SECTION:096
###########################################################

# Auxiliar functions

# The function valid_seq() will check if the given sequence is valid or not.
# seq: is a string containing the sequence entered by the user
def valid_seq(seq):
isvalid = False
#Checks which of the inputs is valid.
for s in seq:
if (s == 'A') or (s == 'C') or (s == 'T') or (s == 'G'):
isvalid = True
else:
isvalid = False
break
return isvalid
# the max_nuc() takes four inputs: the nucleotide frequencey in a colum,
# calculate which nucleotide is more frequent
# and returns a list with two elements: the nucleotide with maximum frequency and
its frequency.
# a,b,c,d: are the number of frequencies for each nucleotide
def max_nuc(A,G,C,T):
if A>G and A>C and A>T:
return["A",A]
elif G>A and G>C and G>T:
return ["G",G]
elif C>A and C>G and C>T:
return ["C",C]
elif T>A and T>C and T>G:
return ["T",T]
#########################
# The function load_data, it take as an argument, it input the DNA sequences, save
in the list and return the list
# a: is a number of sequences to be input
def load_data(a):
#Create a counter for the while loop.
counter=a
#Create an empty list named sequences.
sequences=[]
# While loop continues adding entered sequences to list sequences until reached
number of sequences the user input.
while counter > 0:
seq=input("DNA sequence: ")
if valid_seq(seq):
sequences.append(seq)
counter-=1
else:
print("Invalid Input. Try again")
#Created a new list to add all the valid sequences.
validseq=[]
for i in sequences:
if valid_seq(i):
validseq.append(i)
return validseq
# input sequences
# validate sequences
# save list
# return list
#New function to sort the order of the frequencies from greater to least for the
challenge.
def order(l):
#Reverse each element in l, sort l and reverse l again. Then after the list is
sorted reverse l again to get the list from greatest to least.
for element in l:
element.reverse()
l.sort()
l.reverse()
for element in l:
element.reverse()
#return l
return l

# The function count_nucl_freq, it take arguments the load_data,


# contains the frecuencies of the nucleotides for each column
# a: is a list of DNA sequences
def count_nucl_freq(a):
#create an empty list to store each letter's frequency
frequencies=[]
#Another empty list to store the order for the challenge.
bono=[]
#Use for loops to look for the frequency of each letter in each column.
for i in range(0,len(a[0])):
columnfrec=[0,0,0,0]
for j in range(0,len(a)):
let= a[j][i]
if let=="A":
columnfrec[0]=columnfrec[0]+1
elif let=="G":
columnfrec[1]=columnfrec[1]+1
elif let=="C":
columnfrec[2]=columnfrec[2]+1
else:
columnfrec[3]=columnfrec[3]+1
#Append each letter frequency from greater to least for the challenge display.
bono.append(order([["A:",columnfrec[0]], ["G:",columnfrec[1]],
["C:",columnfrec[2]], ["T:",columnfrec[3]] ])) # BONO
#Append each Maximum frequency by column to the list frequencies.
frequencies.append(max_nuc(columnfrec[0], columnfrec[1], columnfrec[2],
columnfrec[3]))
#Return both lists.
return frequencies, bono

# analyze the list by columns


# find nucleotide frecuencies
# find the nucleotide with the maximum number of repetitions for each columm
# append the output from the max_nuc() function to a list Result

# The function find_consensus, it take arguments the count_nucl_freq and return a


consensus sequence
# a: is a you return in count_nucl_freq
def find_consensus(a):
freq_lst=a
consensusString = ""
#For loop to access each element in index 0 in the frequency list done before and
add it to the consensous string.
for element in freq_lst:
#print(element)
x=element[0]
consensusString= consensusString + x
return consensusString

# The function main, your program to start and function calls


def main():
# ask the number DNA sequence
n_seq = int(input('Number of DNA sequences: '))
#call all the function before
list_seq = load_data(n_seq)
list_freq,list_bono = count_nucl_freq(list_seq)
consensus =find_consensus(list_freq)
#display's DNA consensus
print("Consensus:",consensus)
#Display the word challenge
print("Challenge:")
#Create a for loop to display the frequencies of each letter in ech column
counter=1
for col in list_bono:
#Identify and asign a variable to the postion you want to access in the list
named list_bono:
x = col[0][0]
x2= col[0][1]
y = col[1][0]
y2= col[1][1]
z= col[2][0]
z2=col[2][1]
f= col[3][0]
f2= col[3][1]
#Display each column based on the length of the sequence and each letter's
frequency.
print("Col",str(counter)+": ",sep=" ", end="")
counter+=1
print(str(x) +''+ str(x2),end=" ")
print(str(y) +''+ str(y2),end=" ")
print(str(z) +''+ str(z2),end=" ")
print(str(f) +''+ str(f2))

if __name__ == "__main__":
main()

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