def main(path):
path = path.rstrip('/')
group = load_group(path)
dictionary = count_mutations(path, group)
dictionary = aggregate_chars(group, dictionary)
dictionary = OrderedDict(sorted(dictionary.items()))
write_output(path, group, group_num, dictionary)
def main(proj_path, project_id):
global Session, Sample, Variant
engine = create_engine('sqlite:///{}/{}'.format(proj_path, db_filename))
from db_utils import Sample, Variant, Base
Base.metadata.create_all(bind=engine)
Session = sessionmaker(bind=engine)
proj_path = '{}/{}'.format(proj_path, project_id)
sample_list = compile_group.load_group(proj_path)
build_db(proj_path, project_id, sample_list)
def main(proj_path):
path_config = get_config.all()
snpEff_path = '{}/VScope/extensions/{}'.format(path_config['BASE_PATH'], path_config['SNPEFF'])
group = load_group(proj_path)
print('Annotating vcf files')
db_info = load_db_tag(proj_path)
snpeff_group(snpEff_path, db_info, proj_path, group)
print('Counting impact categories')
impact_count(proj_path, group)
def main(proj_path):
group_num = '1'
end = '_p'
group = load_group(proj_path)
dictionary_pair, total = find_singles(proj_path, group,
end) # Change to dict_pair
dictionary_pair, found = find_data(proj_path, group, dictionary_pair, end)
print('Group total muts:', total, found)
combined_dict = combine_dicts(dictionary_pair)
results = analyse(proj_path, group_num, combined_dict, len(group))
write_output(proj_path, group_num, results)
def main(path, threshold):
write_log(path, 'Performing subtraction with a quality threshold of {}'.format(threshold))
group = load_group(path)
ends = ('_p', ) # '_1', '_2',
for end in ends:
dictionary_pair, total = find_singles(path, group, end)
write_log(path, 'Processing {} total single occurrences from end {}'.format(total, end))
dictionary_pair, found = find_data(path, dictionary_pair, total, group, end, threshold)
write_log(path, 'Found records for {} out of {} single occurrences.'.format(found, total))
chars_dict = count_mutations(dictionary_pair[0])
print_dict(chars_dict)
for key, value in count_mutations(dictionary_pair[1]).items(): # Combine indels and snps
chars_dict[key] += value
print_dict(chars_dict)
chars_dict = aggregate_chars([], chars_dict)
chars_dict = rename_chars(chars_dict)
chars_dict = OrderedDict(sorted(chars_dict.items()))
write_chars(path, end, chars_dict)