def run(self): """Execute ice_partial.py all|split|i|merge.""" cmd = self.args.subCommand logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__), cmd=cmd, v=get_version())) cmd_str = "" try: args = self.args obj = None if cmd == "all": sge_opts = SgeOptions(unique_id=args.unique_id, use_sge=args.use_sge, max_sge_jobs=args.max_sge_jobs, blasr_nproc=args.blasr_nproc) obj = IceAllPartials( root_dir=args.root_dir, fasta_filenames=args.fasta_filenames.split(','), ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sge_opts=sge_opts, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn) elif cmd == "one": # Only assign nfl reads in the given input_fasta file to isoforms obj = IcePartialOne(input_fasta=args.input_fasta, ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn, done_filename=args.done_filename, blasr_nproc=args.blasr_nproc, use_finer_qv=args.use_finer_qv) elif cmd == "split": obj = IcePartialSplit(root_dir=args.root_dir, nfl_fa=args.nfl_fa, N=args.N) elif cmd == "i": obj = IcePartialI(root_dir=args.root_dir, i=args.i, ccs_fofn=args.ccs_fofn, blasr_nproc=args.blasr_nproc) elif cmd == "merge": obj = IcePartialMerge(root_dir=args.root_dir, N=args.N) else: raise ValueError( "Unknown command passed to {f}: {cmd}.".format( f=op.basename(__file__), cmd=cmd)) cmd_str = obj.cmd_str() logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str)) obj.run() except: logging.exception("Exiting {cmd_str} with return code 1.".format( cmd_str=cmd_str)) return 1 return 0
def run(self): """Execute ice_partial.py all|split|i|merge.""" cmd = self.args.subCommand logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__), cmd=cmd, v=get_version())) cmd_str = "" try: args = self.args obj = None if cmd == "all": sge_opts = SgeOptions(unique_id=args.unique_id, use_sge=args.use_sge, max_sge_jobs=args.max_sge_jobs, blasr_nproc=args.blasr_nproc) obj = IceAllPartials(root_dir=args.root_dir, fasta_filenames=args.fasta_filenames.split(','), ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sge_opts=sge_opts, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn) elif cmd == "one": # Only assign nfl reads in the given input_fastq file to isoforms obj = IcePartialOne(input_fastq=args.input_fastq, ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn, done_filename=args.done_filename, blasr_nproc=args.blasr_nproc, use_finer_qv=args.use_finer_qv) elif cmd == "split": obj = IcePartialSplit(root_dir=args.root_dir, nfl_fa=args.nfl_fa, N=args.N) elif cmd == "i": obj = IcePartialI(root_dir=args.root_dir, i=args.i, ccs_fofn=args.ccs_fofn, blasr_nproc=args.blasr_nproc) elif cmd == "merge": obj = IcePartialMerge(root_dir=args.root_dir, N=args.N) else: raise ValueError("Unknown command passed to {f}: {cmd}.". format(f=op.basename(__file__), cmd=cmd)) cmd_str = obj.cmd_str() logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str)) obj.run() except: logging.exception("Exiting {cmd_str} with return code 1.". format(cmd_str=cmd_str)) return 1 return 0