def make_mix(input1, input2, mixtures):
    """ Create mix of input files for mixtures"""
    uid1 = get_uid(input1)
    uid2 = get_uid(input2)
    input_root = uid1 + "-" + uid2
    subprocess.call(["mkdir", "-p", input_root])

    # mix_sam_list = []
    for i in mixtures:
        mix_root = input_root + "/" + input_root + "_" + str(i)
        subprocess.call(["mkdir", "-p", mix_root + "/tmp"])
        subprocess.call(["mkdir", "-p", mix_root + "/logs"])

        out_root_name = input_root + "_" + str(i) + ".sam"
        output1 = mix_root + "/tmp/Sample_" + out_root_name
        output2 = mix_root + "/tmp/Contam_" + out_root_name
        mix_out = mix_root + "/" + input_root + "_" + str(i) + ".sam"
        # mix_sam_list.append([mix_out, input_root + "_" + str(i)])
        out1_file = open(output1, "w")
        out2_file = open(output2, "w")

        subprocess.call(["samtools", "view", "-Sh", "-s", str(i), input1], stdout=out1_file)
        assert os.path.isfile(output1), "File %s not found" % output1

        subprocess.call(["samtools", "view", "-Sh", "-s", str(1 - i), input2], stdout=out2_file)
        assert os.path.isfile(output2), "File %s not found" % output2

        append_sam_file(mix_out, [output1, output2])
        assert os.path.isfile(mix_out), "File %s not found" % mix_out

        subprocess.call(["rm", "-r", mix_root + "/tmp"])
        pathoid_command(mix_out, "", input_root + str(i))
def mix_pathoid(mix_sam):
    mix_id = mix_sam.re.replace(".sam", "-sam-report.tsv")
    pathoid_command(mix_sam, mix_id)
    assert os.path.isfile(mix_id), "File %s not found" % mix_id