README.md

OT_code_test

Requirements

• Requires Python 3.6+.
• Other dependecies are in requirements.txt.

Usage

For problem A

Codes are in code_test.py.

To see the usage:

python code_test.py -h

For problem B

Codes are in process_json.py.

To see the usage:

python process_json.py -h

Runtime on the example evidence file is about 17mins.

Output

The output CSV file of the example evidence file is evidence_stats.txt.gz in folder output.

My code prints count of target pairs on screen:

$ time python process_json.py -i ~/Downloads/17.12%2F17.12_evidence_data.json.gz -o output/evidence_stats.txt --count
number of target pairs sharing connection to at least two diseases:  121114622

real	16m22.277s
user	15m56.546s
sys	0m10.792s

Testing

Due to the time constrain, only one function of process_json is tested (not thoroughly though).