Python Script

This is the process we went through to apply the processes we learned during BASH scripting, but using Python.

In a text editor save as KnockKnock.py

Write a shell that has a user input data then repeat the data back – knock knock joke. Therefore replace QUESTION and JOKE with your own content.

RESPONSE = raw_input(“QUESTION: ”)

print(“JOKE” + RESPONSE)

#Save the script to your USB drive

In your terminal: change directory to your USB drive then run your script.

python KnockKnock.py

In a text editor save as Movie.py

#Ask user for their NAME and AGE.  You will need to apply the technique used for the knockknock.py

if AGE > 17:

     print NAME + “ can see a rated R movie” 

elif AGE < 17 and AGE > 12:

     print NAME + “ can see a rated PG-13 movie”

else:

     print NAME + “ can only see rated PG movies”

In your terminal run your script.

python Movie.py

Test your program for the ages of 33, 18, 16, & 10.

Challenge, how can you make a interactive program that guides the user through a full knock knock joke?

Hint: Prepare the user for how they can respond by providing a clue or options before they input a response. You could also try to add a loop that requires the correct answer to continue the joke.

• print("You are Batman's sidekick")
• RESPONSE = raw_input("Who's there? ")
• print(RESPONSE + "...Who?")
• RETORT = raw_input()
• print("Robin you- hand over the cash!")

Write a program to determine the GC content of a DNA sequence.

Credit and appreciation to Blake Allen for base code and idea.

# -*- coding: utf-8 -*-

#First line of this program sets the unicode for the shell script Python 2 and 3 have different defaults

FILE = raw_input("What file? (Use complete file path) ")

GENE = open(FILE, "r")

#Set nucleotide count to 0

g=0; a=0; c=0; t=0;

#Skip fasta header line

GENE.readline()

for LINE in GENE:

     LINE = LINE.lower()

     for CHAR in LINE:

          if CHAR == "g":

               g+=1

          if CHAR == "a":

               a+=1

          if CHAR == "c":

               c+=1

          if CHAR == "t":

               t+=1

print "number of g's " + str(g) 

print "number of c's " + str(c)

print "number of a's " + str(a)

print "number of t's " + str(t)

#0. = convert to floating point

print "Sequence length: " + str(a+t+c+g)

gc = (g +c+0.)/(a+t+c+g+0.)

print "GC content: " + str(gc)

To apply the above program download a fasta file from NCBI database.

You can use Staphylococcus aureus and Thermus aquaticus as examples. What can be inferred about their niche environment based on the difference in GC content of the 16S rRNA gene?

Some reading as background about GC content <here>