Prereqs

• Python3.8
• pip3.8
• virtualenv
• a sample fasta file (e.g. dna_files/sample.fasta)

Setup

1. mkdir venv
2. virtualenv venv -p python3.8
3. pip3.8 install -r requirements.txt
4. make run

Result Format

• Results are in dna_files/results
• Each result file follows this naming convention:
  • {input_name}.d{dist}_c{count_of_top_unique_seq}_g{num_groups}_t{total_input_seq}.fasta
  • e.g. sample.d1_c740_g40_t805.fasta

Notes (Updated: Dec 20, 2019)

• Each string contains 4 letters, and letters can only be A, T, C, G.
• Each string is ~200 letters.
• Each file contains ~10k strings.
• Similarity is dependent on the position of the letter, and not just based of # of similar letters.
• If 190/200 of a string of 200 characters are the same, then we consider them as the same.

Requirements

• Read all strings from a fasta file, and find unique strings (don't need to compare strings across different files).
• Find similar strings, and group them together (e.g. AATT and AAAT, etc).
• Use % for similarity.

Sample Output

> sample-23 seq appeared 740 times
aaccgg
> sample-25 seq appeared 30 times
aacggg
> sample-80 seq appeared 3 times
ccaagg
...