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 consolidate_miso_across_samples(main_dir, sample_dir_names_list,
chromo, master_fnames_list,
output_path):
'''
For each file in master_fnames_list:
Read inside main_dir/sample_dir/chromo/misofile for all sample_dirs.
1) read the header and write a combined header to the output_path
(meaning adding up all the counts).
2) write sampled_psi and log_score to output_path for each
sample.
TODO: is it weird to put csv writer obj into a function?
'''
# This will be inefficient, because I will open each file twice...
file_count = 0
for f in master_fnames_list:
# Construct fullpath for output file, make directory if does not exist.
# Path will look like output_path/chr1/
chr_out_path = make_dir(os.path.join(output_path, chromo))
with open(os.path.join(chr_out_path, f), 'wb') as writefile:
writer = csv.writer(writefile, delimiter='\t')
# Write summary header of file (loops through all samples)
write_combined_miso_header(sample_dir_names_list, main_dir,
chromo, f, writer)
# Write sampled_psi and log_score for each sample:
write_combined_psi_logscore(sample_dir_names_list,
main_dir,
chromo,
f, writer)
file_count += 1
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
