sicuellar / archerdx_challenge

🔬 Archerdx Code Challenge 🔬

This particular code challenge was split into three parts

1. Recursively find all FASTQ files in a directory and report each file name and the percent of sequences in that file that are greater than 30 nucleotides long.
2. Given a FASTA file with DNA sequences, find 10 most frequent sequences and return the sequence and their counts in the file.
3. Given a chromosome and coordinates, write a program for looking up its annotation. Keep in mind you'll be doing this annotation millions of times. Input: Tab-delimited file: ChrPosition GTF formatted file with genome annotations. Output: Annotated file of gene name that input position overlaps. Hint: Most of the sequence reads come from a small portion of the genome. Try to use this information to improve performance, if possible.

The following repo contains a Ruby and a Python (currently under construction) directory that each contain the challenges in their corresponding languages.

Depndancies

This project is using the follwing

• ruby version 2.5.3

Install

• clone repo here
• cd into the desired code directory Ruby or Python
• cd into desired script numbered above
• run the lib/runner.rb file and follow the instructions on placing analysis file in the correct location.

Testing

To run test enter the desired script as instructed above and run the test/script_name_test.rb file

Personal Information

• LinkedIn click here
• Personal Website click here(under construction)
• GitHub click here
• Twitter click here
• Turing Portfolio click here

archerdx_challenge's Issues

How to download git-lfs files