def netsurfp_rsa(dataset):
netsurfp_dir = os.environ['NETSURFP_DIR']
original_dir = os.getcwd()
os.chdir(netsurfp_dir)
system_call('rm -rf ./temp/')
system_call('mkdir temp')
os.chdir('./temp')
pnet.utils.write_dataset(dataset,
os.path.join(netsurfp_dir, 'temp/temp.seq'))
command = '../netsurfp -i temp.seq -a >temp.rsa'
system_call(command)
path = os.path.join(netsurfp_dir, 'temp/temp.rsa')
os.chdir(original_dir)
with open(path, 'r') as f:
lines = f.readlines()
lines = [line.split() for line in lines]
start = 0
length = len(dataset.sequences[0])
for i, line in enumerate(lines):
if len(line) == 10 and line[3] == '1' and line[0] in ['B', 'E']:
start = i
break
data = np.array(lines[start:start + length])
seq = ''.join(list(data[:, 1]))
assert str(seq) == str(dataset.sequences[0])
rsa = data[:, 4]
return np.array(np.reshape(rsa, newshape=(-1, 1)), dtype=float)
def raptorx_ss(dataset):
raptorx_dir = os.environ['RAPTORX_DIR']
original_dir = os.getcwd()
os.chdir(raptorx_dir)
system_call('rm temp.seq')
system_call('rm -rf ./tmp/temp/')
pnet.utils.write_dataset(dataset, os.path.join(raptorx_dir, 'temp.seq'))
command = './oneline_command.sh temp.seq'
system_call(command)
path = os.path.join(raptorx_dir, 'tmp/temp/temp.ss3')
os.chdir(original_dir)
return read_ss(path, dataset, order=[5, 4, 3])
def psspred_ss(dataset):
psspred_dir = os.environ['PSSPRED_DIR']
original_dir = os.getcwd()
os.chdir(psspred_dir)
system_call('rm -rf ./temp/')
system_call('mkdir temp')
os.chdir('./temp')
pnet.utils.write_dataset(dataset, os.path.join(psspred_dir,
'temp/temp.seq'))
command = 'perl ../PSSpred.pl temp.seq'
system_call(command)
path = os.path.join(psspred_dir, 'temp/seq.dat.ss')
os.chdir(original_dir)
return read_ss(path, dataset, order=[3, 5, 4])