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 __ensure_directory(self, number=0):
hotspot_dir = "%s/hotspots" % self.project_config['output_dir']
bash.make_dir(hotspot_dir)
config_mongo.change_config_field('hotspot_dir', hotspot_dir)
directory = '%s/%s' % (hotspot_dir, number)
bash.make_dir(directory)
return directory
def __init__(self):
self.project_config = config_mongo.get_project_config()
self.logger = Logger.get_logger()
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 __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']