def run_seqnoise(runner, fasta_file, pnoise_mapping, sigma, cutoff, stub, use_m=False, lookup_file=None): m = run.executable_transformer(use_m) # SeqDist seqdist_out = runner.path_join(stub + '.seqdist') with open(seqdist_out, 'w') as fp: runner.run(['SeqDist', '-in', os.path.abspath(fasta_file)], stdout=fp) runner.run([m('FCluster'), '-in', seqdist_out, '-out', stub]) fcluster_list = stub + '.list' # SeqNoise cmd = [ m('SeqNoise'), '-in', os.path.abspath(fasta_file), '-din', seqdist_out, '-out', stub, '-lin', fcluster_list, '-min', os.path.abspath(pnoise_mapping), '-c', cutoff, '-s', sigma ] if lookup_file: cmd.extend(('-rin', lookup_file)) runner.run(cmd)
def run_pyronoise(runner, dat_path, sigma, cutoff, output_stub, use_m=False, lookup_name=None): m = run.executable_transformer(use_m) pnoise_stub = output_stub + '-pnoise' runner.run(['PyroDist', '-in', dat_path, '-out', output_stub]) runner.run([m('FCluster'), '-in', output_stub + '.fdist', '-out', output_stub + '-initial']) cmd = [m('PyroNoise'), '-din', dat_path, '-out', pnoise_stub, '-lin', output_stub + '-initial.list', '-s', sigma, '-c', cutoff] if lookup_name: cmd.extend(('-rin', lookup_name)) runner.run(cmd)
def run_pyronoise(runner, dat_path, sigma, cutoff, output_stub, use_m=False, lookup_name=None): m = run.executable_transformer(use_m) pnoise_stub = output_stub + '-pnoise' runner.run(['PyroDist', '-in', dat_path, '-out', output_stub]) runner.run([ m('FCluster'), '-in', output_stub + '.fdist', '-out', output_stub + '-initial' ]) cmd = [ m('PyroNoise'), '-din', dat_path, '-out', pnoise_stub, '-lin', output_stub + '-initial.list', '-s', sigma, '-c', cutoff ] if lookup_name: cmd.extend(('-rin', lookup_name)) runner.run(cmd)
def run_seqnoise(runner, fasta_file, pnoise_mapping, sigma, cutoff, stub, use_m=False, lookup_file=None): m = run.executable_transformer(use_m) # SeqDist seqdist_out = runner.path_join(stub + '.seqdist') with open(seqdist_out, 'w') as fp: runner.run(['SeqDist', '-in', os.path.abspath(fasta_file)], stdout=fp) runner.run([m('FCluster'), '-in', seqdist_out, '-out', stub]) fcluster_list = stub + '.list' # SeqNoise cmd = [m('SeqNoise'), '-in', os.path.abspath(fasta_file), '-din', seqdist_out, '-out', stub, '-lin', fcluster_list, '-min', os.path.abspath(pnoise_mapping), '-c', cutoff, '-s', sigma] if lookup_file: cmd.extend(('-rin', lookup_file)) runner.run(cmd)