classes_hapiur.py

#takes in a phind file output by hapiur and writes classes file
import argparse
import os
import re

def read_ref(anc):
    anc_set = set()
    anc = open(anc)
    for line in anc:
        anc_set.add(line.strip()) #split?
    return(anc_set)

def main(args):
    ref = args.ref.strip().split(',')
    
    ancs = []
    for anc in ref:
        ancs.append(read_ref(anc))
    
    ind_order = []
    out = open(args.out, 'w')
    phind = open(args.phind)
    for line in phind:
        line = line.strip().split()[0].split(':')[1].rsplit('_', 1)[0]
        ind_order.append(line)
        in_ref = 0
        for anc in range(len(ancs)):
            in_ref = in_ref + int(line in ancs[anc])
            if line in ancs[anc]:
                out.write(str(anc + 1) + ' ')
        print line + ': ' + str(in_ref)
        if in_ref == 0:
            out.write('0 ')
    out.write('\n')
    out.close()

if __name__ == '__main__':
    parser = argparse.ArgumentParser()

    parser.add_argument('--ref', required=True)
    parser.add_argument('--phind', required=True)
    parser.add_argument('--out', required=True)
    
    args = parser.parse_args()

    main(args)