def main(): parser = argparse.ArgumentParser("lookup bait and target intervals") # Logging flags. parser.add_argument( "-d", "--debug", action="store_const", const=logging.DEBUG, dest="level", help="Enable debug logging." ) parser.set_defaults(level=logging.INFO) parser.add_argument("--uuid", required=True, help="uuid string") parser.add_argument("--bam_path", required=True) parser.add_argument("--bam_library_key_json_path", required=False) parser.add_argument("--key_interval_json_path", required=False) # setup required parameters args = parser.parse_args() bam_path = args.bam_path uuid = args.uuid bam_library_key_json_path = args.bam_library_key_json_path key_interval_json_path = args.key_interval_json_path tool_name = "sra_hs_lookup" logger = pipe_util.setup_logging(tool_name, args, uuid) engine = pipe_util.setup_db(uuid) sra_hs_lookup.sra_hs_lookup(bam_path, bam_library_key_json_path, key_interval_json_path, engine, logger) return
def test_setup_db_with_postgres(): """Setting up database connection works with postgres. """ engine = pipe_util.setup_db(uuid.uuid4(), username='******', host='localhost', port=5432, db='prod_bioinfo', ) # TODO perform additional inspection of database setup assert engine, 'database engine not returned'
def main(): parser = argparse.ArgumentParser('CRAMtools bam-style-index') # Logging flags. parser.add_argument('-d', '--debug', action = 'store_const', const = logging.DEBUG, dest = 'level', help = 'Enable debug logging.', ) parser.set_defaults(level = logging.INFO) # Required flags. parser.add_argument('-r', '--reference_fasta_path', required = False, help = 'Reference fasta path.', ) parser.add_argument('-b', '--cram_path', required = False, action="append", help = 'Source cram path.', ) parser.add_argument('-u', '--uuid', required = True, help = 'analysis_id string', ) parser.add_argument('--tool_name', required = True, help = 'cramtools' ) args = parser.parse_args() tool_name = args.tool_name uuid = args.uuid logger = pipe_util.setup_logging(tool_name, args, uuid) engine = pipe_util.setup_db(uuid) hostname = os.uname()[1] logger.info('hostname=%s' % hostname) if tool_name == 'index': cram_path = pipe_util.get_param(args, 'cram_path') reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path') index(uuid, cram_path, reference_fasta_path, engine, logger) else: sys.exit('No recognized tool was selected')
def main(): parser = argparse.ArgumentParser('bamutil docker tool') # Logging flags. parser.add_argument('-d', '--debug', action = 'store_const', const = logging.DEBUG, dest = 'level', help = 'Enable debug logging.', ) parser.set_defaults(level = logging.INFO) # Required flags. parser.add_argument('--tool_name', required = True, help = 'bamutil tool' ) parser.add_argument('--uuid', required = True, help = 'uuid string', ) # Tool flags parser.add_argument('--bam_path', required = False ) # setup required parameters args = parser.parse_args() tool_name = args.tool_name uuid = args.uuid logger = pipe_util.setup_logging(tool_name, args, uuid) engine = pipe_util.setup_db(uuid) be_lenient = True if tool_name == 'splitbam': bam_path = pipe_util.get_param(args, 'bam_path') splitbam(uuid, bam_path, engine, logger) else: sys.exit('No recognized tool was selected') return
def main(): parser = argparse.ArgumentParser('GATK MuTect2 Panel Of Normal creation') # Logging flags. parser.add_argument('-d', '--debug', action = 'store_const', const = logging.DEBUG, dest = 'level', help = 'Enable debug logging.', ) parser.set_defaults(level = logging.INFO) # Required flags. parser.add_argument('-r', '--reference_fasta_path', required = False, help = 'Reference fasta path.', ) parser.add_argument('-rf', '--reference_fasta_fai', required = False, help = 'Reference fasta fai path.', ) parser.add_argument('-snp', '--known_snp_vcf_path', required = False, help='Reference SNP path.', ) parser.add_argument('-cos', '--cosmic_path', required = False, help='Reference COSMIC path.', ) parser.add_argument('-b', '--cram_path', required = False, action="append", help = 'Source cram path.', ) parser.add_argument('-v', '--vcf_path', required = False, action="append", help = 'Individual VCF path', ) parser.add_argument('-j', '--thread_count', required = False, type = is_nat, help = 'Maximum number of threads for execution.', ) parser.add_argument('-bs', '--Parallel_Block_Size', type = is_nat, default = 50000000, required = False, help = 'Parallel Block Size', ) parser.add_argument('-u', '--uuid', required = True, help = 'analysis_id string', ) parser.add_argument('--tool_name', required = True, help = 'gatk tool' ) args = parser.parse_args() tool_name = args.tool_name uuid = args.uuid thread_count = str(args.thread_count) Parallel_Block_Size = str(args.Parallel_Block_Size) logger = pipe_util.setup_logging('gatk_' + tool_name, args, uuid) engine = pipe_util.setup_db(uuid) hostname = os.uname()[1] logger.info('hostname=%s' % hostname) if tool_name == 'mutect2_pon_tool': cram_path = pipe_util.get_param(args, 'cram_path')[0] known_snp_vcf_path = pipe_util.get_param(args, 'known_snp_vcf_path') cosmic_path = pipe_util.get_param(args, 'cosmic_path') reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path') thread_count = pipe_util.get_param(args, 'thread_count') fai_path = pipe_util.get_param(args, 'reference_fasta_fai') blocksize = pipe_util.get_param(args, 'Parallel_Block_Size') mutect2_pon_tool.pon(uuid, cram_path, thread_count, reference_fasta_path, cosmic_path, fai_path, blocksize, known_snp_vcf_path, engine, logger) elif tool_name == 'CombineVariants': vcf_path_list = pipe_util.get_param(args, 'vcf_path') reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path') thread_count = pipe_util.get_param(args, 'thread_count') CombineVariants.combinevcf(uuid, vcf_path_list, reference_fasta_path, engine, logger) else: sys.exit('No recognized tool was selected')