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)
