Bioinformatics_Coding_Task

Solutions to the bioinformatics take-home coding task.

About the author:

Collin Barraugh

Ph.D. Candidate | National Renewable Energy Laboratory Biosciences Center

Colorado School of Mines Advanced Energy Systems AES Doctoral Program

C: (858) 213 - 4014

E: collinbarraugh@gmail.com

LinkedIn: https://www.linkedin.com/in/collin-barraugh-4200b1100

Install

To install the dependencies in the .yml file:

conda env create

conda activate bioinformatics_task

python setup.py develop

Or install with pip:

pip install --editable=git+https://github.com/collinbarraugh/bioinformatics_coding_task.git

If you edit the .yml file with new packages to install, just use:

conda env update

Testing

For tests to run you will need to add the sample_files directory containing the sample .fasta, .fastq, coordinates to annotate .tsv, and gene annotations .gtf files.

/bioinformatics_coding_task/sample_files

Then verify your installation is correct by running the entire test suite:

pytest -s -v tests/

You can also run individual tests for each of the problems:

Problem 1: pytest -s -v tests/problem1

Problem 2: pytest -s -v tests/problem2

Problem 3: pytest -s -v tests/problem3

Usage

If you would like to use these programs from the command line, let me know and I will implement.

Organization

1. sample_files: Not included; you need to add this in order to run tests.

2. src/programs: Folder of solutions to the problems.

- *problem1.py*:


- *problem2.py*:


- *problem3.py*:

3. tests: Test solutions to problems, inputs, outputs, and edge cases.

- *problem1*:


  - *test_problem1.py*: Runs test over additional subdirectories created by *test_case_generator.py*.


  - **expanded_fastq**: Folder populated by *test_case_generator.py* with additional directories over which to perform file search.


- *problem2*:


  - *test_problem2.py*: Runs test over sample fasta.


- *problem3*:


  - *test_problem3.py*: Runs test over .tsv of genetic coordinates and .gtf of annotations.

4. annotated_coordinates.tsv: Annotated coordinates answer key created by problem3.py

5. test_case_generator.py: Populates new directories with .fastq files created by randomly sampling from the orginal files provided