def t_test_and_pickle(fnames_dic, chromo, output_dir, group_1_samples,
group_2_samples, main_dir, queue_obj, min_counts):
'''
Combines several modules together into one so that the process
can be easily multithreaded.
Return a dictionary containing chromosomes as keynames as fnames as values.
'''
# Define constants
pval_str = 'pval'
event_str = 'event'
# Define output dic
# DEBUG
fnames_dic = {}
# Create directory to store pickled dictionary.
make_dir(os.path.join(output_dir, chromo))
'''
# Get list of AS events that need to be t-tested.
# Run the function on the lists separately to ensure
# that each list contains at least one element.
# This means our master_fnames_list is guaranteed to
# have one sample in each group.
'''
group_1_fnames_list = get_all_fnames(group_1_samples, main_dir, chromo)
group_2_fnames_list = get_all_fnames(group_2_samples, main_dir, chromo)
master_fnames_list = group_1_fnames_list + group_2_fnames_list
# Remove repeats
master_fnames_list = list(set(master_fnames_list))
# master_fnames_size = len(master_fnames_list)
# Do t-test between the two groups.
fnames_pickled_list = []
count = 0
for fname in master_fnames_list:
count += 1
# Get dictionary containing psi information for all samples.
psi_info_dic, _ = get_psi_dic_across_samples(fname, group_1_samples,
group_2_samples, main_dir,
chromo, output_dir,
min_counts)
# Add pval and event to dic
psi_info_dic[pval_str] = [t_test_psi_info(psi_info_dic)]
# Remove .miso from fname to get event name.
psi_info_dic[event_str] = [fname.split('.')[0]]
# Save dictionary as a pickle file.
# add .pickle to fname
pickled_fname = ''.join([fname, '.pickle'])
output_fullpath = os.path.join(output_dir, chromo, pickled_fname)
fnames_pickled_list.append(
save_dic_as_pickle(psi_info_dic, output_fullpath))
# save fnames list to output dic
if chromo not in fnames_dic:
fnames_dic[chromo] = fnames_pickled_list
else:
print('Warning, overwriting fnames_list in %s' % chromo)
print('T-tested %s events in %s' % (count, chromo))
queue_obj.put(fnames_dic) # For multithreading
def t_test_and_pickle(fnames_dic, chromo, output_dir, group_1_samples, group_2_samples,
main_dir, queue_obj, min_counts):
'''
Combines several modules together into one so that the process
can be easily multithreaded.
Return a dictionary containing chromosomes as keynames as fnames as values.
'''
# Define constants
pval_str = 'pval'
event_str = 'event'
# Define output dic
# DEBUG
fnames_dic = {}
# Create directory to store pickled dictionary.
make_dir(os.path.join(output_dir, chromo))
'''
# Get list of AS events that need to be t-tested.
# Run the function on the lists separately to ensure
# that each list contains at least one element.
# This means our master_fnames_list is guaranteed to
# have one sample in each group.
'''
group_1_fnames_list = get_all_fnames(group_1_samples, main_dir, chromo)
group_2_fnames_list = get_all_fnames(group_2_samples, main_dir, chromo)
master_fnames_list = group_1_fnames_list + group_2_fnames_list
# Remove repeats
master_fnames_list = list(set(master_fnames_list))
# master_fnames_size = len(master_fnames_list)
# Do t-test between the two groups.
fnames_pickled_list = []
count = 0
for fname in master_fnames_list:
count += 1
# Get dictionary containing psi information for all samples.
psi_info_dic, _ = get_psi_dic_across_samples(fname,
group_1_samples,
group_2_samples,
main_dir, chromo,
output_dir,
min_counts)
# Add pval and event to dic
psi_info_dic[pval_str] = [t_test_psi_info(psi_info_dic)]
# Remove .miso from fname to get event name.
psi_info_dic[event_str] = [fname.split('.')[0]]
# Save dictionary as a pickle file.
# add .pickle to fname
pickled_fname = ''.join([fname, '.pickle'])
output_fullpath = os.path.join(output_dir, chromo, pickled_fname)
fnames_pickled_list.append(save_dic_as_pickle(psi_info_dic,
output_fullpath))
# save fnames list to output dic
if chromo not in fnames_dic:
fnames_dic[chromo] = fnames_pickled_list
else:
print('Warning, overwriting fnames_list in %s' %chromo)
print('T-tested %s events in %s' %(count, chromo))
queue_obj.put(fnames_dic) # For multithreading
def main():
parser = OptionParser()
parser.add_option('-1', '--group1_file', dest='group_1_samplenames_file',
help='Filename containing group 1 sample names (PCa)')
parser.add_option('-2', '--group2_file', dest='group_2_samplenames_file',
help='Filename containing group 2 sample names (NEPC)')
parser.add_option('-d', '--main_directory', dest='main_dir',
help='Main directory containing miso output results.')
parser.add_option('-o', '--output_directory', dest='output_dir',
help='Output directory of t-test results.')
parser.add_option('-O', '--output_filename', dest='output_fname',
help='Output filename of the t-test results.')
parser.add_option('-m', '--min_counts', type='int', dest='min_counts',
help='Minimum junction read counts to be considered '\
'into the t-test. Best practices says 10.')
# Parse options
(options, _) = parser.parse_args()
# Define constants from options
group_1_samplenames_file = options.group_1_samplenames_file
group_2_samplenames_file = options.group_2_samplenames_file
main_dir = options.main_dir
output_dir = options.output_dir
output_fname = options.output_fname
min_counts = options.min_counts
# Define constants
summary_fullpath = os.path.join(output_dir, output_fname)
# Get sample names from textfile.
group_1_samples = get_sample_names_from_file(group_1_samplenames_file)
group_2_samples = get_sample_names_from_file(group_2_samplenames_file)
# Create list of chromosomes.
chr_list = create_chromo_list(prefix='chr')
# chr_list = ['chr11']
# Subset list for only those that contain miso outputs.
group_1_samples = check_if_empty_dir(main_dir, group_1_samples, chr_list)
group_2_samples = check_if_empty_dir(main_dir, group_2_samples, chr_list)
# Init fnames dic
fnames_dic = {}
# Run on multiple threads.
q = Queue()
process_list = []
for chromo in chr_list:
print('Sending %s job to core...' %chromo)
p = Process(target=t_test_and_pickle,
args=(fnames_dic, chromo, output_dir,
group_1_samples, group_2_samples,
main_dir, q, min_counts))
process_list.append(p)
p.start()
for chromo in chr_list:
fnames_dic.update(q.get())
# Wait for all threads to be done before continuing.
for p in process_list:
p.join()
print('Completed %s jobs.' %len(chr_list))
# Write fnames_dic as pickle file.
pickle_filename = ''.join([output_fname, '_filenames_dic.pickle'])
fnames_savepath = os.path.join(output_dir, pickle_filename)
print('Saving filenames_dic.pickle to %s' %fnames_savepath)
pickle_path = save_dic_as_pickle(fnames_dic, fnames_savepath)
# Write information from pickle to textfile.
print('Writing information from pickle to textfile.')
# Read pickle file to get fnames_dic
fnames_dic = read_pickle(pickle_path)
# Read and write to file.
read_pickle_write_to_file(summary_fullpath, chr_list, fnames_dic,
filter_events=True)
print('Summary file saved in: %s' %summary_fullpath)
def main():
parser = OptionParser()
parser.add_option('-1',
'--group1_file',
dest='group_1_samplenames_file',
help='Filename containing group 1 sample names (PCa)')
parser.add_option('-2',
'--group2_file',
dest='group_2_samplenames_file',
help='Filename containing group 2 sample names (NEPC)')
parser.add_option('-d',
'--main_directory',
dest='main_dir',
help='Main directory containing miso output results.')
parser.add_option('-o',
'--output_directory',
dest='output_dir',
help='Output directory of t-test results.')
parser.add_option('-O',
'--output_filename',
dest='output_fname',
help='Output filename of the t-test results.')
parser.add_option('-m', '--min_counts', type='int', dest='min_counts',
help='Minimum junction read counts to be considered '\
'into the t-test. Best practices says 10.')
# Parse options
(options, _) = parser.parse_args()
# Define constants from options
group_1_samplenames_file = options.group_1_samplenames_file
group_2_samplenames_file = options.group_2_samplenames_file
main_dir = options.main_dir
output_dir = options.output_dir
output_fname = options.output_fname
min_counts = options.min_counts
# Define constants
summary_fullpath = os.path.join(output_dir, output_fname)
# Get sample names from textfile.
group_1_samples = get_sample_names_from_file(group_1_samplenames_file)
group_2_samples = get_sample_names_from_file(group_2_samplenames_file)
# Create list of chromosomes.
chr_list = create_chromo_list(prefix='chr')
# chr_list = ['chr11']
# Subset list for only those that contain miso outputs.
group_1_samples = check_if_empty_dir(main_dir, group_1_samples, chr_list)
group_2_samples = check_if_empty_dir(main_dir, group_2_samples, chr_list)
# Init fnames dic
fnames_dic = {}
# Run on multiple threads.
q = Queue()
process_list = []
for chromo in chr_list:
print('Sending %s job to core...' % chromo)
p = Process(target=t_test_and_pickle,
args=(fnames_dic, chromo, output_dir, group_1_samples,
group_2_samples, main_dir, q, min_counts))
process_list.append(p)
p.start()
for chromo in chr_list:
fnames_dic.update(q.get())
# Wait for all threads to be done before continuing.
for p in process_list:
p.join()
print('Completed %s jobs.' % len(chr_list))
# Write fnames_dic as pickle file.
pickle_filename = ''.join([output_fname, '_filenames_dic.pickle'])
fnames_savepath = os.path.join(output_dir, pickle_filename)
print('Saving filenames_dic.pickle to %s' % fnames_savepath)
pickle_path = save_dic_as_pickle(fnames_dic, fnames_savepath)
# Write information from pickle to textfile.
print('Writing information from pickle to textfile.')
# Read pickle file to get fnames_dic
fnames_dic = read_pickle(pickle_path)
# Read and write to file.
read_pickle_write_to_file(summary_fullpath,
chr_list,
fnames_dic,
filter_events=True)
print('Summary file saved in: %s' % summary_fullpath)