def run(self):
paths = env.get_db_locations()
try:
result = subprocess.check_output(['makeblastdb', '-in', self.fasta, '-dbtype', 'prot', '-parse_seqids',
'-title', self.target_name, '-out', self.target_name], cwd=paths[0],
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
result = e.output
def run(self):
paths = env.get_db_locations()
try:
result = subprocess.check_output([
'makeblastdb', '-in', self.fasta, '-dbtype', 'prot',
'-parse_seqids', '-title', self.target_name, '-out',
self.target_name
],
cwd=paths[0],
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
result = e.output
return unicode(result)
def populate(self):
try:
paths = env.get_db_locations()
result = ''
for path in paths:
print path
if len(path) > 1:
dbs = subprocess.check_output(['blastdbcmd', '-list', path])
result += dbs
raw_dbs = result.split('\n')
# each line looks like: F:\path\to\db\db_name db_type -> db_name
self.available_dbs = [os.path.basename(x.split()[0]) for x in raw_dbs[:-1]]
except TypeError, e: # paths is None
# need to return this as a list so that it can populate the drop-down menu
self.available_dbs = ['None, check variable: {}'.format(e.message)]
def populate(self):
try:
paths = env.get_db_locations()
result = ''
for path in paths:
print(path)
if len(path) > 1:
dbs = subprocess.check_output(
['blastdbcmd', '-list', path])
result += dbs
raw_dbs = result.split('\n')
# each line looks like: F:\path\to\db\db_name db_type -> db_name
self.available_dbs = [
os.path.basename(x.split()[0]) for x in raw_dbs[:-1]
]
except TypeError as e: # paths is None
# need to return this as a list so that it can populate the drop-down menu
self.available_dbs = ['None, check variable: {}'.format(e.message)]
