def run(self): """Run""" iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=None, fasta_fofn=None, sge_opts=None, prog_name="ice_quiver_merge") iceq.add_log(self.cmd_str()) iceq.add_log("root_dir: {d}.".format(d=self.root_dir)) iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N)) src = [ iceq.submitted_quiver_jobs_log_of_chunk_i(i=i, num_chunks=self.N) for i in range(0, self.N) ] for f in src: if not nfs_exists(f): raise IOError("Log {f} ".format(f=f) + "of submitted quiver jobs does not exist.") dst = iceq.submitted_quiver_jobs_log iceq.add_log( "Collecting submitted quiver jobs from:\n{src}\nto {dst}.".format( src="\n".join(src), dst=dst)) cat_files(src=src, dst=dst) iceq.close_log()
def run(self): """Run""" iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=None, fasta_fofn=None, sge_opts=None, prog_name="ice_quiver_merge") iceq.add_log(self.cmd_str()) iceq.add_log("root_dir: {d}.".format(d=self.root_dir)) iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N)) src = [iceq.submitted_quiver_jobs_log_of_chunk_i(i=i, num_chunks=self.N) for i in range(0, self.N)] for f in src: if not nfs_exists(f): raise IOError("Log {f} ".format(f=f) + "of submitted quiver jobs does not exist.") dst = iceq.submitted_quiver_jobs_log iceq.add_log("Collecting submitted quiver jobs from:\n{src}\nto {dst}.". format(src="\n".join(src), dst=dst)) cat_files(src=src, dst=dst) iceq.close_log()
def run(self): """Run""" cmd_str = self.cmd_str() iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=self.bas_fofn, fasta_fofn=self.fasta_fofn, sge_opts=self.sge_opts, prog_name="ice_quiver_{i}of{N}". format(i=self.i, N=self.N)) iceq.add_log(cmd_str) iceq.add_log("root_dir: {d}.".format(d=self.root_dir)) iceq.add_log("Index of chunks: i = {i}.".format(i=self.i)) iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N)) iceq.validate_inputs() iceq.process_chunk_i(i=self.i, num_chunks=self.N) iceq.close_log()