def add(self):
adder = Add()
if self.args['one_sample'] is not None:
new_sample = [tuple(entry.strip('}').strip('{').strip(',').split(':')) for entry in self.args['one_sample']]
new_sample = dict(new_sample)
adder.add_one_sample(new_sample)
if len(self.args['email']) > 0:
if not sampleinfo_mongo.is_fully_annotated(new_sample['SAMPLE']):
annotate = Annotate()
annotate.annotate_sample(new_sample['SAMPLE'], 'orig')
output_files = Output()
final_file = output_files.sample_variants_csv(new_sample['SAMPLE'], 'orig')
message = "Here are all the variants for the sample %s with their QC status." % new_sample['SAMPLE']
for address in self.args['email']:
self.__log_sending_email(address)
output_bash.email_file(message, final_file, address)
elif self.args['sample_info'] is not None:
adder.add_sample_info(self.args['sample_info'])
def output(self):
if self.args['type'] == 'sample':
if not sampleinfo_mongo.is_fully_annotated(self.args['name']):
annotate = Annotate()
annotate.annotate_sample(self.args['name'], 'orig')
output_files = Output()
output_files.sample_variants_csv(self.args['name'], 'orig')
def output(self):
# The output option handler that will write the sample_variants_csv containing important information about
# the sample variants.
if self.args['type'] == 'sample':
if self.args['name'] == "all":
output_files = Output()
output_files.output_all_variants()
else:
if not sampleinfo_mongo.is_fully_annotated(self.args['name']):
annotate = Annotate()
annotate.annotate_sample(self.args['name'], 'orig')
output_files = Output()
output_files.sample_variants_csv(self.args['name'], 'orig')
def add(self):
"""
This carries out the appropriate operation if add is selected from the parser.
:return:
"""
adder = Add()
# This is the adding procedure performed for when one sample is added from the command line.
if self.args['one_sample'] is not None:
new_sample = [tuple(entry.strip('}').strip('{').strip(',').split(':')) for entry in self.args['one_sample']]
new_sample = dict(new_sample)
# The adder actually adds the sample to the database.
adder.add_one_sample(new_sample)
# This is what is carried out if an email is desired, it will actually peform an additional
# annotation to make sure that the result has all of the necessary information.
if len(self.args['email']) > 0:
if not sampleinfo_mongo.is_fully_annotated(new_sample['SAMPLE']):
annotate = Annotate()
annotate.annotate_sample(new_sample['SAMPLE'], 'orig')
output_files = Output()
final_file = output_files.sample_variants_csv(new_sample['SAMPLE'], 'orig')
# This actually carries out the emailing.
message = "Here are all the variants for the sample %s with their QC status." % new_sample['SAMPLE']
for address in self.args['email']:
self.__log_sending_email(address)
output_bash.email_file(message, final_file, address)
# This is how the samples are added from a file of many samples.
elif self.args['sample_info'] is not None:
adder.add_sample_info(self.args['sample_info'])