remap_2_to_col_ids_to_third.py

import sys
fn = sys.argv[1]
ls_list = []
mapping = {}
with open(fn, 'r') as inp:
    for n, line in enumerate(inp):
        ls = line.split('\t|\t')
        assert len(ls) == 5
        assert ls[-1] == '\n'
        if n > 0:
            uid = ls[0]
            name = ls[2]
            assert uid not in mapping
            mapping[uid] = name
        ls_list.append(ls)

out = sys.stdout
for n, ls in enumerate(ls_list):
    if n > 0:
        ls[0] = mapping[ls[0]]
        if ls[1]:
              ls[1] =mapping[ls[1]]
    out.write('\t|\t'.join(ls))