def perform_hotspot(self):
self.project_config = config_mongo.get_project_config()
hotspot_file = self.project_config['hotspot_file']
hotspot_dir = self.project_config['hotspot_dir']
output_dir = hotspot_dir + "/hotspot_output"
if os.path.isdir(output_dir):
self.__log_hotspot_files_already_exist()
else:
bash.make_dir(output_dir)
ref_fasta = self.project_config['ref_fasta']
bed_file = self.project_config['project_bed']
tvc_params = self.project_config['tvc_params']
bam_files = sampleinfo_mongo.get_bam_files()
# HOTSPOT ALL OF THE BAM FILES
self.__hotspot_bam_files(bam_files, hotspot_file, output_dir, ref_fasta, bed_file, tvc_params)
# Delete the filter files
all_files = glob(output_dir+"/*")
for vcf in all_files:
if "filtered.vcf" in vcf:
bash.remove_file(vcf)
def __init__(self):
self.project_config = config_mongo.get_project_config()
self.logger = Logger.get_logger()
self.output_files_dir = '%s/output_files' % self.project_config['output_dir']
if 'output_files_dir' not in self.project_config or not os.path.isdir(self.project_config['output_files_dir']):
bash.make_dir(self.output_files_dir)
config_mongo.change_config_field('output_files_dir', self.output_files_dir)
else:
self.output_files_dir = self.project_config['output_files_dir']
def reconcile_hotspot_and_database(self, hotspot_file):
self.project_config = config_mongo.get_project_config()
client, db = mongo.get_connection()
vcf_reader = vcf.Reader(open(hotspot_file, 'r'))
for rec in vcf_reader:
chrom, pos, ref, alt = int(rec.CHROM.strip("chr")), int(rec.POS), rec.REF, [str(alt) for alt in rec.ALT]
if not hotspot_mongo.is_hotspot(chrom, pos, ref, alt, db):
self.__reconcile(chrom, pos, ref, alt, db)
client.close()
def __init__(self):
"""
This init method is different in that it will create the annotation_dir config parameter if it doesn't
already exist. This is not necessarily the most elegant way to do this, but it works.
:return:
"""
self.project_config = config_mongo.get_project_config()
self.logger = Logger.get_logger()
# Creates the annotation_dir if needed and loads it into the config file
self.annotations_dir = '%s/annotations' % self.project_config['output_dir']
if 'annotation_dir' not in self.project_config or not\
os.path.isdir(self.project_config['annotation_dir']):
bash.make_dir(self.annotations_dir)
config_mongo.change_config_field('annotation_dir', self.annotations_dir)
else:
self.annotations_dir = self.project_config['annotation_dir']
def main(self, args):
"""
This is the main function that runs Variant manager according to the arguments that were passed in by
the user.
:param args: These are the args as parsed by the parser at the bottom of this script.
:return: None
"""
# This sets the project name for several different modules to use.
self.args = args
varman2.set_project_name(args['project_name'])
# Checks the arguments given to make sure that they can be processed correctly.
self.__argcheck(args)
# Setting up the project config file
self.__setup_project_analysis(self.args)
self.project_config = config_mongo.get_project_config()
# SETTING UP LOGGING
Logger.create_logger(self.project_config['log_file'], 'a')
self.logger = Logger.get_logger()
# This executes the correct argument specified by the user
argexecute = ArgExecutor(self.args)
if self.args['which'] == 'add':
argexecute.add()
elif self.args['which'] == 'delete':
argexecute.delete()
elif self.args['which'] == 'load':
argexecute.load_variants()
elif self.args['which'] == 'hotspot':
argexecute.hotspot()
elif self.args['which'] == 'stats':
argexecute.stats()
elif self.args['which'] == 'output':
argexecute.output()
elif self.args['which'] == 'nothing':
argexecute.nothing()
def save_annotations(self, annovar_vcf):
self.__log_saving_annotations()
self.project_config = config_mongo.get_project_config()
client, db = mongo.get_connection()
with open(annovar_vcf, "r") as annov_in:
line = annov_in.readline()
if not line.startswith("#CHROM"):
while line.startswith('##'):
line = annov_in.readline()
header = line.strip().strip("#").split("\t")
for line in annov_in:
chrom, pos, ref, alt, annotations = self.__process_annovar_line(line, header)
annotate_mongo.save_annotation(chrom, pos, ref, alt, annotations, db)
client.close()
def save_annotations(self, annovar_vcf):
"""
This will save the annotations of a sample in the database.
:param annovar_vcf:
:return:
"""
self.__log_saving_annotations()
self.project_config = config_mongo.get_project_config()
client, db = mongo.get_connection()
with open(annovar_vcf, "r") as annov_in:
line = annov_in.readline()
if not line.startswith("#CHROM"):
while line.startswith('##'): # this reads through the junk lines
line = annov_in.readline()
header = line.strip().strip("#").split("\t")
for line in annov_in:
line = line.strip()
if line != "":
chrom, pos, ref, alt, annotations = self.__process_annovar_line(line, header)
annotate_mongo.save_annotation(chrom, pos, ref, alt, annotations, db)
else:
header = line.strip().strip("#").split("\t")
for line in annov_in:
line = line.strip()
if line != "":
chrom, pos, ref, alt, annotations = self.__process_annovar_line(line, header)
annotate_mongo.save_annotation(chrom, pos, ref, alt, annotations, db)
client.close()
def __init__(self):
self.project_config = config_mongo.get_project_config()
self.logger = Logger.get_logger()
def __init__(self, var_type):
self.project_config = config_mongo.get_project_config()
self.logger = Logger.get_logger()
self.variant_type = var_type
self.affected_dict = sampleinfo_mongo.get_affected_dict()
