Files you need to read:
ecoli.fasta : The data file for your submission.
short.fasta : A data file to debug your code. Do not use for submission.
Files you need to submit:
Your filenames need to start with ‘problem1’ or ‘problem2’. For each problem, submit:
- A properly commented and PEP8-compliant Python file for the module.
- A properly commented and PEP8-compliant Python file for the script.
- A PDF of the terminal output using the print icon in the lower left corner in PyCharm.
- One screenshot of your terminal showing the git commands you typed.
- One screenshot of your internet browser showing your Python files in GitHub.
Problem 1. Count the Bases (50 points)
Write a module with a function that takes a filename, tests whether the file extension is .fasta, prints the number of As, Cs, Gs, and Ts found in the sequence if it is a fasta file, and throws an exception if the input is not a fasta file. Use a single space between the upper case letter and the count.
Write a script that uses this module and shows the number of bases in ecoli.fasta in the terminal. Were you to process short.fasta, you should see the following in your terminal.
Problem 2. Count Bigrams (50 points)
Without reusing the code you wrote for Problem 1, write a new module and a new script. Your code need to show the number of pairs of DNA bases in ecoli.fasta in the terminal using the function printDigrams provided in the lecture slides. You might want to practice using short.fasta , but your final submission needs to use ecoli.fasta. The second line is
which has the pairs AG, GC, CT, TT, TT, TT, TC in order, and so on.
Create a dictionary that maps strings to the number of times the string appears. AA appears 338006 times in the file ecoli.fasta
If you count the bases in that sample file short.fasta and print the result, you would get the following: AA appears 18 times, AG appears 9 times, and so on.
In your terminal, include a short description with each output, e.g. “The result is:”. The output should not exceed 100 lines.
A G C T
A 18 9 8 12
G 7 6 9 9
C 7 3 3 13
T 14 13 7 15
Rubric (50 points per problem):
– (10 points) Your submission include all files listed under ‘Files you need to submit’. Files have meaningful names and the content matches the filename.
– (10 points) The code reads the correct data, not the sample data, and generates the correct results in the terminal.
– (10 points) Exceptions and explicit error messages are used to cover common error cases, e.g. trying to read a file that doesn’t exist or trying to read a file with the wrong extension.
– (10 points) Code is commented and PEP8 compliant. Variable names are meaningful. Every module and function has a meaningful docstring.
– (10 points) Concepts covered in the last lecture are used. Unnecessary structures, global variables, hard-coded values, break, and continue are not used. Code, results, and test results are easy to read.
Thank you so much!Life saver!
Awesome paper! Very reliable and prompt
This was great!
Thank you. I will get back to you next week. There are more classes that I need help.
Thanks a lot. All good
I loved the service it was really fast & efficient. I ended up with an A in my class!
It was a pleasure working with you. You are really responsible and always do you’re best and of course, we will keep working together.
The essay and the Excel file looks good. Thank you for working with me throughout the project.
Thank you for the quick help. I was stuck.
You are a lifesaver. Thank you. I will be needing your help for the midterm exam.
I am very grateful for your help. Without you, I would have quit a long time ago. Appreciate your help 100%.
I know it is APA 7 and it should not have the running headers, but my professor insists on them. Please include them in the upcoming orders. Overall, I liked it and I will be submitting it tonight. Thank you.
Thank you for the help. All good.
You do an exceptional job, have gotten good grades n positive feedback/ comments from my professors since you started helping me.
Thanks. I will handle the replies.
Simple Order Process
Fill in the Order Form
Share all the assignment information. Including the instructions, provided reading materials, grading rubric, number of pages, the required formatting, deadline, and your academic level. Provide any information and announcements shared by the professor. Choose your preferred writer if you have one.
Get Your Order Assigned
Once we receive your order form, we will select the best writer from our pool of experts to fit your assignment.
Share More Data if Needed
You will receive a confirmation email when a writer has been assigned your task. The writer may contact you if they need any additional information or clarifications regarding your task
Let Our Essay Writer Do Their Job
Once you entrust us with your academic task, our skilled writers embark on creating your paper entirely from the ground up. Through rigorous research and unwavering commitment to your guidelines, our experts meticulously craft every aspect of your paper. Our process ensures that your essay is not only original but also aligned with your specific requirements, making certain that the final piece surpasses your expectations.
Quality Checks and Proofreading
Upon the completion of your paper, it undergoes a meticulous review by our dedicated Quality and Proofreading department. This crucial step ensures not only the originality of the content but also its alignment with the highest academic standards. Our seasoned experts conduct thorough checks, meticulously examining every facet of your paper, including grammar, structure, coherence, and proper citation. This comprehensive review process guarantees that the final product you receive not only meets our stringent quality benchmarks but also reflects your dedication to academic excellence.
Review and Download the Final Draft
If you find that any part of the paper does not meet the initial instructions, send it back to us with your feedback, and we will make the necessary adjustments.