def main(argv):
args = get_args(argv)
# input arguments
m = args['m']
n = args['n']
num_mutes = args['num_mutes']
directory = os.path.dirname(os.path.realpath(__file__))
# for num_mutes in [10, 50, 100]:
# for m in [1, 3, 5, 10]:
# for n in [2, 3, 4, 5]:
# print 'n:', n, 'm:', m, 'num_mutes:', num_mutes
size_mutes = args['size_mutes']
metaFile = args['meta_file']
output_folder = args['output_folder']
constants_dict = dict()
constants_dict['mut_types'] = ['amp', 'rem', 'inv']
constants_dict[
'exp_mut_size'] = size_mutes # default exp_mut_size is 5745000
constants_dict['exp_mut_count'] = num_mutes / (2 * n - 2)
constants_dict['cov'] = 20
constants_dict['read_len'] = 300
constants_dict['num_patients'] = 5
# remove chrom_dict later
chrom_dict = dict()
chrom_dict[('1', 0)] = chpr.ChrmProf(248956422)
chrom_dict[('1', 1)] = chpr.ChrmProf(248956422)
chrom_dict[('2', 0)] = chpr.ChrmProf(242193529)
chrom_dict[('2', 1)] = chpr.ChrmProf(242193529)
chrom_dict[('3', 0)] = chpr.ChrmProf(198295559)
chrom_dict[('3', 1)] = chpr.ChrmProf(198295559)
# sub_folder_name = 'n_' + str(n) + '_m_' + str(m) + '_l_' + str(num_mutes)
for patient_idx in range(1, 1 + constants_dict['num_patients']):
patient_folder_name = 'patient' + str(patient_idx)
# outputFolder = directory + '/sim_data' + '/' + sub_folder_name + '/' + patient_folder_name
outputFolder = output_folder + '/' + patient_folder_name
# clean up existing files under outputFolder
if os.path.exists(outputFolder):
shutil.rmtree(outputFolder)
os.makedirs(outputFolder)
l = random_get_tree(n) # list
edge_list = get_edges(l)
gp = gnpr.GeneProf(chrom_dict, constants_dict)
t = Tree(edge_list, gp)
geneprof_list = list()
t.add_mutations_along_edges(t.rootNode, geneprof_list)
generate_t(t, 'T.dot', outputFolder)
U = random_get_usages(m, 2 * n - 1)
l, sv_cn_idx_dict = get_bp_copy_num_idx_dict(t, n, constants_dict)
r, seg_cn_idx_dict, seg_bgn_idx_dict, seg_end_idx_dict = get_seg_copy_num_idx_dict(
t, n)
C = generate_c(t, n, constants_dict)
c_p, c_m = generate_seg_cp_paternal(t, n)
F = generate_f(U, C)
a, h, mate_dict = get_a_h_mate_dict(t, n, constants_dict)
output_tsv(U, '/U.tsv', outputFolder)
output_tsv(C, '/C.tsv', outputFolder)
output_tsv(F, '/F.tsv', outputFolder)
generate_s(metaFile, t, l, sv_cn_idx_dict, r, seg_cn_idx_dict,
seg_bgn_idx_dict, seg_end_idx_dict, F, U, C, c_p, c_m, a, h,
mate_dict, outputFolder)
# test_random_tree(n, repeat_time)
l = [1, [1, 1]]
edge_list = sm.get_edges(l)
print(l)
print(edge_list)
###################
# Test tree class #
###################
print('Test tree class:')
chrom_dict = dict()
chrom_dict[('1', 0)] = chpr.ChrmProf("AAABBBCCCDDDEEEFFF")
chrom_dict[('1', 1)] = chpr.ChrmProf("AAABBBCCCDDDEEEFFF")
chrom_dict[('2', 0)] = chpr.ChrmProf("RRRRRSSSSSTTTTTUUUUUVVVVV")
chrom_dict[('2', 1)] = chpr.ChrmProf("RRRRRSSSSSTTTTTUUUUUVVVVV")
chrom_dict[('3', 0)] = chpr.ChrmProf("XXXXYYYYZZZZ")
chrom_dict[('3', 1)] = chpr.ChrmProf("XXXXYYYYZZZZ")
constants_dict = dict()
constants_dict['mut_types'] = ['amp', 'rem', 'inv']
constants_dict['mut_size_mean'] = 5
constants_dict['mut_size_var'] = 2
constants_dict['mut_count_mean'] = 3
constants_dict['mut_count_var'] = 1
constants_dict['cov'] = 20
import chrm_prof as chpr
import pprint
pp = pprint.PrettyPrinter(indent=2)
cp = chpr.ChrmProf("AAABBBCCCDDDEEEFFF")
print('')
print(cp.amp(4, 10))
cp.pprint()
print('')
print(cp.amp(11, 13))
cp.pprint()
print('')
print(cp.amp(2, 19))
cp.pprint()
print('')
print(cp.rem(0, 6))
cp.pprint()
print('')
print(cp.rem(2, 8))
cp.pprint()
print('')
print(cp.amp(9, 25))
cp.pprint()
print('')