Figure 2 creates a line graph comparing the relative codon adaptiveness of ENST00000198536.7 wildtype Paired Immunoglobulin type 2 receptor alpha (PILRA) gene versus rs2405442:T>C mutant PILRA isoform. It uses the speeds of both the wildtype and mutant PILRA sequence provided by the user.
Input: Wildtype and mutant speeds fasta files created by ExtRamp https://github.com/ridgelab/ExtRamp
Output: Figure 2 png file saved to outputfigs/ directory (user must create this directory)
IN THIS ORDER WITH SPACES IN BETWEEN EACH ARGUMENT
- name of tissue or cell with underscores in between each word
- wildtype speeds fasta file
- mutant speeds fasta file
Example command:
python3 figure2.py Amygdala PILRA_ramp/Manuscript/wtspeedsamygdala.fasta PILRA_ramp/Manuscript/mtspeedsamygdala.fasta
The output should match Amygdala.png in the expected outputs directory.
figure2.py uses Python version 3.6
Python Libraries:
- sys
- pandas
- numpy
- matplotlib.pyplot
- argparse
- os