GEN220_2025

GEN220 High Throughput Data Analysis

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Homework 2

Practicing Python

You will accept the homework problem invitation through google classroom. The link is in canvas.

This will create a hw2-python-practice-yourname repository. You will clone this repository to your system or open in visual studio

$ git clone git@github.com:biodataprog/hw2-python-practice-YOURNAME.git

I have created starter scripts for you to update and add the necessary code to solve the problem.

  1. Write a UNIX script which has the job of setting up the data. It will be called setup.sh a. Have it download the Thermus aquaticus genome from NCBI, available at this url: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/399/775/GCF_001399775.1_ASM139977v1/GCF_001399775.1_ASM139977v1_genomic.fna.gz. b. Have it download the Bacillus subtilis genome at this url: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/045/GCF_000009045.1_ASM904v1/GCF_000009045.1_ASM904v1_genomic.fna.gz c. uncompress the files

  2. Write a python script called ‘problem1.py’

    a. Have your python script calculate the percent GC (number of G and C bases in the sequence file divided by the total length of the sequence) content the two files downloaded above. Print out the GC percentage for each of the files.

    Bonus - make the script more generic to print out filename and GC content for any set of files passed in on the command line

  3. Write a script called ‘problem2.py’ reads in file sequences.txt.

    a. It has several columns, have it print out a new report to STDOUT with three columns: GeneID, gene length (gDNA column), mRNA length

    Bonus: print the data sorted so the longest gene (gDNA) comes first and smallest is last.

  4. Write a script called ‘problem3.py’ reads in file sequences.txt.

    a. Generate a summary table of statistics about gene length - what is the average length, longest and shortest genes b. have the script create file that contains a summary of gene sizes binned by 500bp. Say there were 4 genes in the file of lengths 1100, 750, 1800, 950. You print out the following to a file called ‘lengths_binned.csv’

       bin_size,count
   0,0
   500,2
   1000,1
   1500,1