def _check_database(self, database):
#Database file does not exist
if not os.path.isfile(database):
raise BE(code = -5, value = database)
#Database is not formated (if dbformatexe is added in the configuration path it will be autoformated)
formatdb_files = []
if self._search_type == 'nucl': formatdb_sufix = ['.nhr','.nin','.nsq']
elif self._search_type == 'prot': formatdb_sufix = ['.phr','.pin','.psq']
for sufix in formatdb_sufix:
if not os.path.isfile(database + sufix):
formatdb_files.append(database + sufix)
if len(formatdb_files) > 0:
try:
dbexe = Executable(executable = self._configurator.get('blast','dbformatexe'),
path = self._configurator.get('blast','path'),
variable_path = self._configurator.get('blast','variable_path'))
SBIglobals.alert('debug', self, 'Trying to format de DB {0} to perform a blast search.\n'.format(database))
dbexe.add_attribute(database, '-in')
dbexe.add_attribute(self._search_type, '-dbtype')
SBIglobals.alert('debug', self, 'Executing command {0}\n'.format(dbexe))
dbexe.execute()
except ConfigParser.NoOptionError, e:
raise BE(code = -6, value = formatdb_files)
except SystemError, e:
raise BE(code = -11, value = e)
class CDhitExe(object):
def __init__(self, fasta, threshold, output_dir=None, execute=True):
fasta = os.path.abspath(fasta)
if output_dir is None:
output_dir = os.path.split(fasta)[0]
if threshold >= 0.7: word = 5
elif threshold >= 0.6: word = 4
elif threshold >= 0.5: word = 3
elif threshold >= 0.4: word = 2
else: word = 1
#CDhit executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(
os.getenv('SBI_CONFIG_FILE', default_configuration_file))
self._exe = Executable(executable=self._configurator.get(
'cd-hit', 'executable'),
path=self._configurator.get('cd-hit', 'path'))
self._input = fasta
output_file = os.path.split(fasta)[1] + '.' + str(threshold).replace(
'.', '_')
self._output = os.path.join(output_dir, output_file)
self._threshold = str(threshold)
self._word = word
if execute:
self._execute()
@property
def output_file(self):
return self._output + '.clstr'
def _execute(self):
self._exe.add_attribute(self._input, '-i')
self._exe.add_attribute(self._output, '-o')
self._exe.add_attribute(self._threshold, '-c')
self._exe.add_attribute('1', '-g')
self._exe.add_attribute(self._word, '-n')
try:
self._exe.execute(silent=True)
except SystemError, e:
sys.stderr.write(
'Some error occurred while executing cd-hit\n{0}\n'.format(e))