def run_makemat(self):
print "-" * 60
print "Running Makemat"
id = self.config['id']
fasta_file = self.config["path"]["input"]
try:
shutil.copy(fasta_file, self.config['path']['output'])
except shutil.Error:
pass
pn_file = os.path.join(self.config['path']['output'], id + '.pn')
sn_file = os.path.join(self.config['path']['output'], id + '.sn')
with open(pn_file, 'w') as pn_f:
pn_f.write(id + '.chk')
with open(sn_file, 'w') as sn_f:
sn_f.write(id + '.fasta')
args = [self.config['makemat']['command'],
'-P', os.path.join(self.config['path']['output'], id)]
util.run_command(args)
print "Done\n"
def _run(self):
ccmpred_config = self.config['ccmpred']
id = self.config['id']
aln_file = os.path.join(self.config['path']['output'], id + '.aln')
output_file = self.output_file
if self.config['ccmpred']['n_threads'] == 0:
if 'cuda_dev' in self.config['ccmpred']:
args = [self.config['ccmpred']['command'],
'-d', str(self.config['ccmpred']['cuda_dev']),
aln_file,
output_file]
else:
gpu_id = 0
print gpu_id
args = [self.config['ccmpred']['command'],
'-d', str(gpu_id),
aln_file,
output_file]
else:
args = [self.config['ccmpred']['command'],
'-t', str(self.config['ccmpred']['n_threads']),
aln_file,
output_file]
util.run_command(args)
def _run(self):
id = self.config['id']
aln_file = os.path.join(self.config['path']['output'], id + '.aln')
output_file = self.output_file
args = [self.config['freecontact']['command'],
'-a', str(self.config['freecontact']['n_threads']),
'-f', aln_file]
util.run_command(args, output_file)
def _run(self):
id = self.config['id']
input_file = os.path.join(self.config['path']['output'], id + '.a3m')
log_file = self.output_file
hhm_file = os.path.join(self.config['path']['output'], id + '.hhm')
args = [
self.config['hhmake']['command'], '-i', input_file, '-o', hhm_file
]
util.run_command(args, log_file)
def run_hhfilter(self):
id = self.config['id']
pseudo_a3m_file = os.path.join(self.config['path']['output'],
id + '.a3m')
output_file = os.path.join(self.config['path']['output'],
id + '.filtered')
args = [
self.config['hhfilter']['command'], '-id', '90', '-M', 'first',
'-cov', '50', '-i', pseudo_a3m_file, '-o', output_file
]
util.run_command(args)
def run_solvpred(self):
print "-" * 60
print "Running Solvpred"
id = self.config['id']
matrix_file = self.matrix_file
solv_file = self.solv_file
args = [self.config['solvpred']['command'],
matrix_file,
self.config['solvpred']['data']]
util.run_command(args, solv_file)
print "Done\n"
def run_jackhmmer(self):
id = self.config['id']
fasta_file = self.config['path']['input']
output_file = os.path.join(self.config['path']['output'],
id + '.jackali')
log_file = os.path.join(self.config['path']['output'], id + '.jacklog')
args = [
self.config['jackhmmer']['command'], '-N',
str(self.config['jackhmmer']['n_iter']), '--cpu',
str(self.config['jackhmmer']['n_threads']), '--incE',
str(self.config['jackhmmer']['inc_E']), '-A', output_file,
fasta_file, self.config['jackhmmer']['uniref_db']
]
util.run_command(args, log_file)
def run_psipred(self):
print "-" * 60
print "Running PsiPred"
id = self.config['id']
fasta_file = self.config["path"]["input"]
matrix_file = self.matrix_file
ss_file = os.path.join(self.config['path']['output'], id + '.ss')
args = [self.config['psipred']['command'],
matrix_file,
os.path.join(self.config['psipred']['data'], 'weights.dat'),
os.path.join(self.config['psipred']['data'], 'weights.dat2'),
os.path.join(self.config['psipred']['data'], 'weights.dat3')]
util.run_command(args, ss_file)
print "Done\n"
def _run(self):
hh_config = self.config['hhblits']
id = self.config['id']
input_file = self.config['path']['input']
output_file = os.path.join(self.config['path']['output'], id + '.a3m')
log_name = os.path.join(self.config['path']['output'], id + '.hhblog')
args = [
hh_config['command'], '-i', input_file, '-d',
hh_config['uniprot_db'], '-oa3m', output_file, '-o', log_name,
'-n',
str(hh_config['n_iters']), '-maxfilt',
str(hh_config['maxfilt']), '-diff',
str(hh_config['diff']), '-id',
str(hh_config['id']), '-cov',
str(hh_config['cov']), '-e',
str(hh_config['e_value']), '-cpu',
str(hh_config['n_threads'])
]
util.run_command(args)
def run_psipred_pass2(self):
print "-" * 60
print "Running PsiPredPass2"
id = self.config['id']
ss_file = os.path.join(self.config['path']['output'], id + '.ss')
ss2_file = self.ss2_file
horiz_file = os.path.join(self.config['path']['output'], id + '.horiz')
args = [self.config['psipred_pass2']['command'],
os.path.join(self.config['psipred']['data'], 'weights_p2.dat'),
str(self.config['psipred_pass2']['n_iters']),
str(self.config['psipred_pass2']['DCA']),
str(self.config['psipred_pass2']['DCB']),
ss2_file,
ss_file]
util.run_command(args, horiz_file)
print "Done\n"
def run_blast(self):
print "-" * 60
print "Running PSI-BLAST (blastpgp)"
id = self.config['id']
fasta_file = self.config["path"]["input"]
output_name = os.path.join(self.config['path']['output'], id + '.chk')
log_name = os.path.join(self.config['path']['output'], id + '.blast')
blast_config = self.config['blast']
args = [blast_config['command'],
'-a', str(blast_config['n_threads']),
'-b', '0',
'-j', str(blast_config['n_iters']),
'-h', str(blast_config['e_value']),
'-d', str(blast_config['database']),
'-i', fasta_file,
'-C', output_name]
util.run_command(args, log_name)
print "Done\n"