mtx2edgelist.py

#!/usr/bin/env python

"""
    mtx2edgelist.py
"""

from scipy.io import mmread
import numpy as np
import pandas as pd
import argparse

def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument('--inpath', type=str)
    parser.add_argument('--outpath', type=str)
    return parser.parse_args()


if __name__ == '__main__':
    args = parse_args()
    
    print('reading')
    x = mmread(args.inpath)
    
    print('processing')
    edges = np.column_stack([x.row, x.col])
    edges = pd.DataFrame(edges)
    edges = edges.sort_values([0, 1]).reset_index(drop=True)
    
    print('writing')
    edges.to_csv(args.outpath, header=None, sep='\t', index=False)