def import_json(args):
#set up logging
logger = logging.getLogger('snapperdb.snpdb.import_json')
json_path = untar_file(args.json_file)
json_dict = {}
#import json
try:
with open(json_path) as json_data:
json_dict = json.load(json_data)
json_data.close()
except IOError:
print "Issue with JSON file. Exiting."
exit()
#parse config
args.config_file = json_dict['config_file']
config_dict = parse_config(args)
#initalise snpdb class
snpdb = SNPdb(config_dict)
#parse confif
snpdb.parse_config_dict(config_dict)
#get reference genome path
ref_seq_file = os.path.join(snapperdb.__ref_genome_dir__,
snpdb.reference_genome + '.fa')
#read the reference fasta
ref_seq = read_multi_contig_fasta(ref_seq_file)
#create VCF class
vcf = Vcf()
vcf.parse_json_dict(json_dict, ref_seq)
vcf.depth_average = json_dict['strain_stats']
vcf.sample_name = json_dict['sample']
logger.info('Uploading to SNPdb')
#upload vcf
#connect to snpdb postgres
snpdb._connect_to_snpdb()
snpdb.snpdb_conn = psycopg2.connect(snpdb.conn_string)
if args.write_flag == 'W':
snpdb.snpdb_upload(vcf, args)
#annotate vars
logger.info('Annotating new variants')
snpdb.snpdb_annotate_vars(vcf)
elif args.write_flag == 'R':
print "under development"
def get_strains(args, config_dict):
#set up logging
logger = logging.getLogger('snapperdb.snpdb.get_strains')
logger.info('Inititialising SnpDB Class')
#initalise snpdb class
snpdb = SNPdb(config_dict)
#parse confif
snpdb.parse_config_dict(config_dict)
#connect to postgresdb
snpdb._connect_to_snpdb()
snpdb.snpdb_conn = psycopg2.connect(snpdb.conn_string)
#remove isolate
snpdb.get_strain_list(args.thresh)
def accept_outlier(args, config_dict):
#set up logging
logger = logging.getLogger('snapperdb.snpdb.export_json')
logger.info('Inititialising SnpDB Class')
#initalise snpdb class
snpdb = SNPdb(config_dict)
#parse confif
snpdb.parse_config_dict(config_dict)
#connect to postgresdb
snpdb._connect_to_snpdb()
snpdb.snpdb_conn = psycopg2.connect(snpdb.conn_string)
#remove isolate
snpdb.zscore_exception(args.out_strain)
def add_ref_cluster(args, config_dict):
#set up loggging
logger = logging.getLogger('snapperdb.snpdb.add_ref_cluster')
logger.info('Initialising SNPdb class')
#create snpdb class
snpdb = SNPdb(config_dict)
#parse config into snpdb object
logger.info('Parsing config dict')
snpdb.parse_config_dict(config_dict)
#connect to snpdb postgres
snpdb._connect_to_snpdb()
snpdb.snpdb_conn = psycopg2.connect(snpdb.conn_string)
snpdb.add_cluster()
def vcf_to_db(args, config_dict, vcf):
#set up loggging
logger = logging.getLogger('snapperdb.snpdb.vcf_to_db')
logger.info('Initialising SNPdb class')
#create snpdb class
snpdb = SNPdb(config_dict)
#parse config into snpdb object
logger.info('Parsing config dict')
snpdb.parse_config_dict(config_dict)
#connect to snpdb postgres
snpdb._connect_to_snpdb()
snpdb.snpdb_conn = psycopg2.connect(snpdb.conn_string)
#check stack?
if inspect.stack()[0][3] == 'fastq_to_db':
# fastq_to_db we will alread have a vcf object to work wih
logger.info('You are running fastq_to_db.')
elif inspect.stack()[0][3] == 'vcf_to_db':
## there is no existing vcf class here, but there will definitely be a vcf
logger.info('You are running vcf_to_db. Initialising Vcf class.')
vcf = Vcf()
logger.info('Making SNPdb variables and output files')
#set up variables
snpdb.define_class_variables_and_make_output_files(args, vcf)
#read vcf
vcf.read_multi_contig_vcf()
logger.info('Uploading to SNPdb')
#upload vcf
snpdb.snpdb_upload(vcf, args)
#annotate vars
logger.info('Annotating new variants')
snpdb.snpdb_annotate_vars(vcf)