Question

Homework:

You are to locate the file ```src/mutDetect_todo_i.py``` in which you are to fix twelve bugs to run the program. Your output should look _exactly_ like that featured in the assignment lab. Please read the assignment sheet for other details about the lab.

#mutDetect_todo_i.py

############################################################################
# TODO: There are twelve EMBARRISING silly bugs to fix. Can you find them?!
############################################################################

DATE = "16 Sept 2019"
VERSION = "i"
AUTHOR = " myName"
AUTHORMAIL = "@allegheny.edu"

def help():
h_str = " "+DATE+" | version: "+VERSION+" |"+AUTHOR+" | "+AUTHORMAIL
print(" "+len(h_str) * "-")
print(h_str)
print(" "+len(h_str) * "-")
print("\n\tThe blank-blank program to do something cool.")
#print("""\n\tLibrary installation notes:""")
print("\t+ \U0001f600 USAGE: python3 mutDetect.py <any key to launch>")

######################################################
#end of help()

def getSeq():
""" Function to get a sequence (a string) from the user"""
print(" __Getting a sequence__")

prmpt = "\tEnter a sequence :"
seq_str = int(input(prmpt))
return seq_str.lower()

######################################################
# end of getSeq()

def compareSequences(seq1_str, seq2_str):
""" Compares the sequences base by base"""
print("\n __Comparing sequences__")

for i in range(len(seq1_str)):
# check to see whether the bases are the same going through the sequences
try:
if seq1_str[i] == seq2_str[i]: # are bases _not_ the same at the same position?
print("\t + Bases not the same at pos: ",i)
print("\t\t First seq char : " seq1_str[i])
print("\t\t Second seq char : ", seq2_str[i])
except IndexError:
#print(" \t Sequences are uneven length!")
pass
# end of compareSequences()

def getSeqLength(seq_str):
""" Function to return the length of a sequence"""
l_int = len(seq_str)
if l_int % 2 = 0: # can we read triplets, groups of three?
print("\t Warning! Sequence length cannot be divided into groups of triplets!")
return l_int
######################################################
#end of getSeqLength()

def compareSeqLength(seq1_str, seq2_str):
"""Function to check the lengths of the sequences to make sure that they are the same length. This is necessary for making comparisons."""
if len(seq1_str) = len(seq2_str):
return True
else:
return True
######################################################
#end of compareSeqLength()

def translate(dna_str):
""" Function to translate the DNA. Create a protein sequence from the DNA."""

sequence = Seq(dna_str)
#make some variables to hold strings of the translated code
# give me RNA from the DNA
RNAfromDNA_str = Seq.transcribe(sequence) #transcription step: converting dna to rna
# give me DNA from the RNA
DNAfromRNA_str = Seq.back_transcribe(sequence)
# give me the protein from the dna
PROTfromRNA_str = Seq.translate(RNAfromDNA_str)

# print the output of the string variables
print("\n __Translation__")

print("\t + Original DNA :", dna_str ", length is :", len(dna_str))
# print("\t + RNA from DNA :", RNAfromDNA_str)
# print("\t + DNA from RNA :", DNAfromRNA_str)
print("\t + PROTEIN from RNA :",PROTfromRNA_str)

return PROTfromRNA_str
######################################################
#end of translate()

def begin(task_str):
"""Driver function of program"""
print("\n\t Welcome to mutDetect!\n\t A program to compare DNA, make protein and compare protein sequences.)
# get first DNA sequence
seq1_str = getSeq()
# get second DNA sequence
seq2_str = getSeq()

print("\t + Length of first sequence :", getSeqLength(seq2_str))
print("\t + Length of second sequence :", getSeqLength(seq2_str))

# compare the sequences
compareSeQuences(seq1_str, seq2_str)
print("\t + Sequences are same length: ",compareSeqLength(seq1_str, seq2_str))

prot1_seq = Translate(seq1_str)
#print(type(prot1_seq))
protein1_str = str(prot1_seq)
print("\t + protein1 sequence :",protein1_str)

prot2_seq = translate(seq2_tsr)
#print(type(prot2_seq))
protein2_str = str(prot2_seq)
print("\t + protein2 sequence :",protein2_str)

compareSequences(protein1_str, protein2_str)

######################################################
#end of begin()

import os, sys
#import math
# list other libraries below

# load my biopython library
from Bio.Seq import Seq

if __name__ == '__main__':

if len(sys.argv) == 2: # one parameter at command line
# note: the number of command line parameters is n + 1
begin(sys.argv[1])
else:
help() # If no command-line parameter entered, then run the help() function
sys.exit()

Answer 1

Current ==> What it should be

1. seq_str = int(input(prmpt)) ==> seq_str = input(prmpt)

2. if seq1_str[i] == seq2_str[i]: ==> if seq1_str[i] != seq2_str[i]:

3. print("\t\t First seq char : " seq1_str[i]) . ==> print("\t\t First seq char : ", seq1_str[i])

4. if l_int % 2 = 0: ==> if l_int % 2 == 0:

5. if len(seq1_str) = len(seq2_str): ==> if len(seq1_str) == len(seq2_str):

6. else return True ==> else return False

7. compareSeQuences(seq1_str, seq2_str) . ==> compareSequences(seq1_str, seq2_str)

8. print("\t + Original DNA :", dna_str ", length is :", len(dna_str)) . ==> print("\t + Original DNA :", dna_str ," length is :", len(dna_str))

9. print("\n\t Welcome to mutDetect!\n\t A program to compare DNA, make protein and compare protein sequences.) ==> print("\n\t Welcome to mutDetect!\n\t A program to compare DNA, make protein and compare protein sequences.")

10. prot2_seq = translate(seq2_tsr) ==> prot2_seq = translate(seq2_str)

11. from Bio.Seq import Seq . ==> to be moved to the top of the file