apa.icount.study

#!/usr/bin/python3

import os
import sys
import apa

maps = {}
f = open(os.path.join(apa.path.root_folder, "icount", "icount.mappings.txt"))
r = f.readline()
while r:
    r = r.replace("\n", "").replace("\r", "")
    if r.endswith(":"):
        lib_id = r.split("/")[0]
        exp_id = r.split("/")[1][1:-1]
    elif r!="":
        map = r
        assert(maps.get(map, None)==None)
        maps[map] = "%s_e%s" % (lib_id, exp_id)
    r = f.readline()
f.close()

print "# generated from icount comps file = %s" % sys.argv[1]
f = open(sys.argv[1], "rt")
header = f.readline().replace("\r", "").replace("\n", "").split("\t")
r = f.readline()
print "\t".join(["id", "control_name", "control_id", "test_name", "test_id"])
comp_id = 1
while r:
    r = r.replace("\r", "").replace("\n", "").split("\t")
    data = dict(zip(header, r))
    cmaps = data["control_ID"].replace(" ", "").replace("\"", "").split(",")
    tmaps = data["test_ID"].replace(" ", "").replace("\"", "").split(",")
    cmaps = [maps[i] for i in cmaps]
    tmaps = [maps[i] for i in tmaps]
    print "\t".join([str(comp_id), data["control_name"], ",".join(cmaps), data["test_name"], ",".join(tmaps)])
    comp_id += 1
    r = f.readline()
f.close()