For this assignment you will write a single Python script that will have several steps &

specific requirements. Be sure your file name includes your last name and module number.

For full credit the script should include comments, run without error and produce correct,

properly formatted output. Partial credit will be given on the following scale:

Runs without error, correct output data, output not formatted

properly

$90\%$

Runs without error, incorrect output data $75\%$

Does not run without errors, code is mostly accurate $60\%$

Does not run without errors, some code is accurate $50\%$

Any of the above, without comments $-10\%$ more

Besides this document, there are two attached files: One is an input file $($cftr$\_$cds$.$fa$),$ the

other $($gen$\_$code.py$)$ contains a full genetic code dictionary that you can copy & paste into

your script.

Your script will open the input file, which is a dna sequence for the CFTR cds region. You

will calculate the percent CG content, transcribe into RNA, translate the RNA into protein

and write the protein sequence to a new text file.

Some additional details:

$$ Write a function to calculate the percent CG content. The function will take a single

argument, a nucleotide sequence and return the percent CG$.$ In the function use this

logic: Percent CG $=(($# of C$$s $+$ # of G$$s$)/$ length of sequence$)*100.$ This will

generate a float with Python$$s standard precision, with a lot of decimal places. Use

the round$()$ function to round the result to $2$ decimal places, before you return the

value. In Spyder, you can get help on the round function syntax by typing

help$($round$)$ in the console $($also known as the interactive shell$).$

$$ After the percent CG content is calculated and returned, use a conditional to check

the value. If it$$s $>40,$ print a message to the screen that states the percent CG

content.

$$ Transcription to RNA is performed by substituting the base $$T$$ with the base $$U$.$

CMBI$-6621/$ BIOL$-4521$

Page $2$ of $2$

$$ Be sure to use $$with$$ when opening your files.

$$ When you write the protein sequence to your file, include a new header that has the

gene name and some additional text that indicates it$$s protein. Format the sequence

so it$$s $60$ characters per line. You by this time have seem several examples of doing

this so you can adapt that example code.

$$ The full genetic code dictionary is provided to save you some typing. You can open

the attached file in Spyder and simply copy & paste the dictionary into your script.

Alternatively, you can save the file in the same directory as your script and import it

into your script with the following command:

from gen$\_$code import gen$\_$code

If you do this, put it at the beginning of your script.