Skip to content

Latest commit

 

History

History
35 lines (24 loc) · 1.04 KB

Figure2README.md

File metadata and controls

35 lines (24 loc) · 1.04 KB

Figure2.py

Purpose

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)

Arguments:

IN THIS ORDER WITH SPACES IN BETWEEN EACH ARGUMENT

  1. name of tissue or cell with underscores in between each word
  2. wildtype speeds fasta file
  3. 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.

Requirements:

figure2.py uses Python version 3.6

Python Libraries:

  1. sys
  2. pandas
  3. numpy
  4. matplotlib.pyplot
  5. argparse
  6. os