sequence stringlengths 1.27k 35.1k | code stringlengths 75 8.58k |
|---|---|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'movefastq'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'};... | def movefastq(self):
logging.info('Moving FASTQ files')
for sample in self.metadata.runmetadata.samples:
outputdir = os.path.join(self.path, sample.name)
fastqfiles = sorted(glob(os.path.join(self.path, '{}_*.fastq*'.format(sample.name)))) \
if sorted(glob(os.path... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'add_raw_entity'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], '... | def add_raw_entity(self, entity: dict) -> dict:
needed_in_entity = set([
'label',
'type',
])
options_in_entity = set([
'label',
'type',
'definition',
'comment',
'superclass',
'synonyms',
'... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17', '19']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'delete_annotation'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '9', '13']}; {'id': '4', 'type': 'identifier', 'c... | def delete_annotation(
self,
term_ilx_id: str,
annotation_type_ilx_id: str,
annotation_value: str) -> dict:
term_data = self.get_entity(term_ilx_id)
if not term_data['id']:
exit(
'term_ilx_id: ' + term_ilx_id + ' does not exist'
)
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'configfilepopulator'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def configfilepopulator(self):
self.forwardlength = self.metadata.header.forwardlength
self.reverselength = self.metadata.header.reverselength
cycles = [[1, self.forwardlength, self.runid],
[self.forwardlength + 1, self.forwardlength + 8, self.runid],
[self.fo... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_check_time_format'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': []... | def _check_time_format(self, labels, values):
for label, value in zip(labels, values):
if value == "*":
continue
if label == "day_of_week":
if isinstance(value, string_types):
if value not in ORDER_WEEK:
raise Pa... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'readlength'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}... | def readlength(self):
logging.info('Estimating read lengths of FASTQ files')
for sample in self.samples:
sample.run.Date = 'NA'
sample.run.InvestigatorName = 'NA'
sample.run.TotalClustersinRun = 'NA'
sample.run.NumberofClustersPF = 'NA'
sample.... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'confirm'}; {'id': '3', 'type': 'parameters', 'children': ['4', '7', '10', '15', '18']}; {'id': '4', 'type': 'default_parameter', 'chi... | def confirm(prompt='Really?', color='warning', yes_values=('y', 'yes'),
abort_on_unconfirmed=False, abort_options=None):
if isinstance(yes_values, str):
yes_values = (yes_values,)
prompt = '{prompt} [{yes_value}/N] '.format(prompt=prompt, yes_value=yes_values[0])
if color:
prompt... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_string'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def from_string(cls, action_str):
args = {}
try:
mod_obj = ast.parse(action_str)
except (SyntaxError, ValueError) as e:
raise e
else:
call_obj = mod_obj.body[0].value
if isinstance(call_obj, ast.Attribute):
module = call_obj... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'epcrparsethreads'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def epcrparsethreads(self):
from Bio import SeqIO
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.epcrparse, args=())
threads.setDaemon(True)
threads.start()
for sample in self.metad... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'trimquality'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'... | def trimquality(self):
logging.info("Trimming fastq files")
with progressbar(self.metadata) as bar:
for sample in bar:
if type(sample.general.fastqfiles) is list:
fastqfiles = sorted(sample.general.fastqfiles)
outputdir = sample.general... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'contamination_finder'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children':... | def contamination_finder(self, input_path=None, report_path=None):
logging.info('Calculating contamination in reads')
if input_path is not None:
input_dir = input_path
else:
input_dir = self.path
if report_path is not None:
reportpath = report_path
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'subclass_genesis'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'valu... | def subclass_genesis(self, genesisclass):
class MayaGenesisWin(genesisclass):
def open_shot(self, taskfile):
return self.open_file(taskfile)
def save_shot(self, jbfile, tf):
self.update_scene_node(tf)
self.save_file(jbfile)
def ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '35', '37']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'override_options'}; {'id': '3', 'type': 'parameters', 'children': ['4', '8', '18', '30']}; {'id': '4', 'type': 'typed_parameter... | def override_options(config: DictLike, selected_options: Tuple[Any, ...], set_of_possible_options: Tuple[enum.Enum, ...], config_containing_override: DictLike = None) -> DictLike:
if config_containing_override is None:
config_containing_override = config
override_opts = config_containing_override.pop("o... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '24', '36']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'determine_selection_of_iterable_values_from_config'}; {'id': '3', 'type': 'parameters', 'children': ['4', '8']}; {'id': '4', 't... | def determine_selection_of_iterable_values_from_config(config: DictLike, possible_iterables: Mapping[str, Type[enum.Enum]]) -> Dict[str, List[Any]]:
iterables = {}
requested_iterables = config["iterables"]
for k, v in requested_iterables.items():
if k not in possible_iterables:
raise Key... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_key_index_object'}; {'id': '3', 'type': 'parameters', 'children': ['4', '8']}; {'id': '4', 'type': 'typed_parameter', 'c... | def create_key_index_object(key_index_name: str, iterables: Dict[str, Any]) -> Any:
for name, iterable in iterables.items():
if iter(iterable) == iter(iterable):
raise TypeError(
f"Iterable {name} is in iterator which can be exhausted. Please pass the iterable"
f"... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '34', '50']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_objects_from_iterables'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '9', '19', '29']}; {'id': '4', 'type'... | def create_objects_from_iterables(obj, args: dict, iterables: Dict[str, Any], formatting_options: Dict[str, Any], key_index_name: str = "KeyIndex") -> Tuple[Any, Dict[str, Any], dict]:
objects = {}
names = list(iterables)
logger.debug(f"iterables: {iterables}")
KeyIndex = create_key_index_object(
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '42', '58']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iterate_with_selected_objects_in_order'}; {'id': '3', 'type': 'parameters', 'children': ['4', '14', '28']}; {'id': '4', 'type':... | def iterate_with_selected_objects_in_order(analysis_objects: Mapping[Any, Any],
analysis_iterables: Dict[str, Sequence[Any]],
selection: Union[str, Sequence[str]]) -> Iterator[List[Tuple[Any, Any]]]:
if isinstance(selection, str):... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'phenotypes_to_scored'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children':... | def phenotypes_to_scored(self,phenotypes=None,overwrite=False):
if not self.is_uniform(): raise ValueError("inconsistent phenotypes")
if phenotypes is None:
phenotypes = self.phenotypes
elif isinstance(phenotypes,str):
phenotypes = [phenotypes]
def _post(binary,p... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'subset'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def subset(self,logic,update=False):
pnames = self.phenotypes
snames = self.scored_names
data = self.copy()
values = []
phenotypes = logic.phenotypes
if len(phenotypes)==0: phenotypes = pnames
removing = set(self.phenotypes)-set(phenotypes)
for k in phenot... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'collapse_phenotypes'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'childr... | def collapse_phenotypes(self,input_phenotype_labels,output_phenotype_label,verbose=True):
if isinstance(input_phenotype_labels,str): input_phenotype_labels = [input_phenotype_labels]
bad_phenotypes = set(input_phenotype_labels)-set(self.phenotypes)
if len(bad_phenotypes) > 0: raise ValueError("E... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'scored_to_phenotype'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def scored_to_phenotype(self,phenotypes):
def _apply_score(scored_calls,phenotypes):
present = sorted(list(set(phenotypes)&set(scored_calls.keys())))
total = sum([scored_calls[x] for x in present])
if total > 1:
raise ValueError("You cant extract phenotypes f... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'spike_times'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [],... | def spike_times(signal, threshold, fs, absval=True):
times = []
if absval:
signal = np.abs(signal)
over, = np.where(signal>threshold)
segments, = np.where(np.diff(over) > 1)
if len(over) > 1:
if len(segments) == 0:
segments = [0, len(over)-1]
else:
if ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bin_spikes'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 's... | def bin_spikes(spike_times, binsz):
bins = np.empty((len(spike_times),), dtype=int)
for i, stime in enumerate(spike_times):
bins[i] = np.floor(np.around(stime/binsz, 5))
return bins |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'corewriter'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}... | def corewriter(self):
printtime('Creating core allele files', self.start)
for gene in sorted(self.genesequence):
self.geneset.add(gene)
genefile = os.path.join(self.coregenelocation, '{}.fasta'.format(gene))
if not os.path.isfile(genefile):
with open(g... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'profiler'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; ... | def profiler(self):
printtime('Calculating core profiles', self.start)
for strain in self.corealleles:
self.coreset.add(tuple(sorted(self.corealleles[strain].items())))
header = 'ST,{}\n'.format(','.join(sorted(self.geneset)))
data = ''
for count, core in sorted(enume... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'row2dict'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']}; {'id': '4', 'type': 'identifier',... | def row2dict(row, depth=None, exclude=None, exclude_pk=None,
exclude_underscore=None, only=None, fk_suffix=None):
if depth == 0:
return None
d, mapper = {}, get_mapper(row)
if depth is None:
depth = getattr(row, ATTR_DEPTH, DEFAULT_DEPTH) - 1
else:
depth -= 1
if ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dict2row'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21']}; {'id': '4', 'type': 'identif... | def dict2row(d, model, rel=None, exclude=None, exclude_pk=None,
exclude_underscore=None, only=None, fk_suffix=None):
if not isinstance(d, dict):
raise TypeError('Source must be instance of dict, got %s instead' %
type(d).__name__)
row = model()
mapper = get_mappe... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '74', '76']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'remote'}; {'id': '3', 'type': 'parameters', 'children': ['4', '13', '14', '17', '20', '23', '26', '29', '32', '42', '45', '55',... | def remote(cmd: arg(container=list),
host,
user=None,
port=None,
sudo=False,
run_as=None,
shell='/bin/sh',
cd=None,
environ: arg(container=dict) = None,
paths=(),
stdout: arg(type=StreamOptions) = None,
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '69', '71']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sync'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '22', '25', '28', '31', '34', '37'... | def sync(source,
destination,
host,
user=None,
sudo=False,
run_as=None,
options=('-rltvz', '--no-perms', '--no-group'),
excludes=(),
exclude_from=None,
delete=False,
dry_run=False,
mode='u=rwX,g=rwX,o=',
quiet=Tr... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '22', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_determine_outliers_for_moving_average'}; {'id': '3', 'type': 'parameters', 'children': ['4', '10', '14', '18']}; {'id': '4', '... | def _determine_outliers_for_moving_average(moving_average: np.ndarray,
moving_average_threshold: float,
number_of_values_to_search_ahead: int,
limit_of_number_of_values_below_threshold: int) ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_dynamic_class'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'va... | def make_dynamic_class(typename, field_names):
if isinstance(field_names, basestring):
field_names = field_names.replace(",", " ").split()
field_names = map(str, field_names)
safe_fields_names = map(_encode_property_name, field_names)
attr = dict((safe_name, _property(name)) for name, safe_name ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'verifyInputs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def verifyInputs(self, mode):
if len(self._aichans) < 1:
failmsg = "Must have at least one input channel selected"
QtGui.QMessageBox.warning(self, "Invalid Setting", failmsg)
return False
if mode == 'chart':
if self.ui.aifsSpnbx.value()*self.fscale > 10000... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'complete'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def complete(command_line,
current_token,
position,
shell: arg(choices=('bash', 'fish'))):
position = int(position)
tokens = shlex.split(command_line[:position])
all_argv, run_argv, command_argv = run.partition_argv(tokens[1:])
run_args = run.parse_args(run_argv)
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'export'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'valu... | def export(context, keywords, module, update):
logging.info(_('Export Mode'))
database = context.obj['sense']
none = True
if update:
exports = OrderedDict()
from .executables.pe import PE
for filename in keywords:
module = split_ext(filename, basename=True)[0]
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_source'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value... | def get_source(label, source_type, **kwargs):
if source_type not in yapconf.ALL_SUPPORTED_SOURCES:
raise YapconfSourceError(
'Invalid source type %s. Supported types are %s.' %
(source_type, yapconf.ALL_SUPPORTED_SOURCES)
)
if source_type not in yapconf.SUPPORTED_SOURCES:... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '37', '39']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_project_observable'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '9', '13', '24', '35']}; {'id': '4', 'type': 'i... | def _project_observable(self, input_key: str,
input_observable: Any,
get_hist_args: Dict[str, Any] = None,
projection_name_args: Dict[str, Any] = None,
**kwargs) -> Hist:
if get_hist_args is None:
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'getrruleset'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def getrruleset(self, addRDate=False):
rruleset = None
for name in DATESANDRULES:
addfunc = None
for line in self.contents.get(name, ()):
if rruleset is None:
rruleset = rrule.rruleset()
if addfunc is None:
a... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list_processed_parameter_group_histogram'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', '... | def list_processed_parameter_group_histogram(self, group=None, start=None, stop=None, merge_time=20):
params = {}
if group is not None:
params['group'] = group
if start is not None:
params['start'] = to_isostring(start)
if stop is not None:
params['sto... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list_completeness_index'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'childre... | def list_completeness_index(self, start=None, stop=None):
params = {}
if start is not None:
params['start'] = to_isostring(start)
if stop is not None:
params['stop'] = to_isostring(stop)
return pagination.Iterator(
client=self._client,
path... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list_packets'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', '... | def list_packets(self, name=None, start=None, stop=None, page_size=500, descending=False):
params = {
'order': 'desc' if descending else 'asc',
}
if name is not None:
params['name'] = name
if page_size is not None:
params['limit'] = page_size
i... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '26']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list_events'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23']}; {'id': '4', 'type': 'ide... | def list_events(self, source=None, severity=None, text_filter=None,
start=None, stop=None, page_size=500, descending=False):
params = {
'order': 'desc' if descending else 'asc',
}
if source is not None:
params['source'] = source
if page_size is... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list_parameter_ranges'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']}; {'id': '4', 'type': '... | def list_parameter_ranges(self, parameter, start=None, stop=None,
min_gap=None, max_gap=None,
parameter_cache='realtime'):
path = '/archive/{}/parameters{}/ranges'.format(
self._instance, parameter)
params = {}
if start is n... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'copy_file'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'chil... | def copy_file(source, destination, unique=False, sort=False, case_sensitive=True, create_path=False):
_File.copy(source, destination, unique, sort, case_sensitive, create_path) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'tree'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [],... | def tree(node, formatter=None, prefix=None, postfix=None, _depth=1):
current = 0
length = len(node.keys())
tee_joint = '\xe2\x94\x9c\xe2\x94\x80\xe2\x94\x80'
elbow_joint = '\xe2\x94\x94\xe2\x94\x80\xe2\x94\x80'
for key, value in node.iteritems():
current += 1
k = formatter(key) if formatter else key
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '4']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run'}; {'id': '3', 'type': 'parameters', 'children': []}; {'id': '4', 'type': 'block', 'children': ['5', '11', '20', '26', '35', '44',... | def run():
args = parse_args()
codetools.setup_logging(args.debug)
git_tag = args.tag
git_email = codetools.lookup_email(args)
git_user = codetools.lookup_user(args)
if not args.manifest_only:
eups_tag = args.eups_tag
if not eups_tag:
eups_tag = eups.git_tag2eups_tag(... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter_seq'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'seq'};... | def filter_seq(seq):
'''Examines unreserved sequences to see if they are prone to mutation. This
currently ignores solely-power-of-2 guides with b > 3'''
if seq.res:
return None
n = nt.Factors(seq.factors)
guide, s, t = aq.canonical_form(n)
seq.guide = guide
cls = aq.get_cla... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'add_data'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sel... | def add_data(self, filenames):
def _parse_table(table):
def _parse_line(line):
return line.split('\t')
lines = (_parse_line(one) for one in table.splitlines()
if re.match(r'^\d', one))
return (remove_false(one) for one in lines)
de... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'check_tags'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def check_tags(repos, tags, ignore_existing=False, fail_fast=False):
debug("looking for {n} tag(s):".format(n=len(tags)))
[debug(" {t}".format(t=t)) for t in tags]
debug("in {n} repo(s):".format(n=len(repos)))
[debug(" {r}".format(r=r.full_name)) for r in repos]
present_tags = {}
absent_tags =... |
{'id': '0', 'type': 'module', 'children': ['1', '42', '44', '46', '48', '50', '52', '54', '56', '58', '61', '82']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8', '37', '39']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'getmlsthelper'}; {'id': '3', 'type': 'parameters', 'chil... | def getmlsthelper(referencefilepath, start, organism, update):
from accessoryFunctions.accessoryFunctions import GenObject
organismset = set()
organism = organism if organism != 'Shigella' else 'Escherichia'
organismdictionary = {'Escherichia': 'Escherichia coli
'Shigella': 'Es... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; ... | def set(self, **kwargs):
self.player_lock.acquire()
if 'acqtime' in kwargs:
self.player.set_aidur(kwargs['acqtime'])
if 'aifs' in kwargs:
self.player.set_aifs(kwargs['aifs'])
self.aifs = kwargs['aifs']
if 'aifs' in kwargs or 'acqtime' in kwargs:
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'readlist'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; ... | def readlist(self):
printtime('Sorting reads', self.start)
for i in range(self.cpus):
threads = Thread(target=self.listread, args=())
threads.setDaemon(True)
threads.start()
for sample in self.runmetadata.samples:
self.listqueue.put(sample)
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'has_change_permission'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'chil... | def has_change_permission(self, page, lang, method=None):
if method != 'POST':
return True
if self.change_page():
return True
if lang:
perm = self.user.has_perm(
'pages.can_manage_%s' % lang.replace('-', '_')
)
if perm:
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'args'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id... | def args(self):
params = self.parameters
args = OrderedDict()
args['help'] = HelpArg(command=self)
normalize_name = self.normalize_name
get_arg_config = self.get_arg_config
get_short_option = self.get_short_option_for_arg
get_long_option = self.get_long_option_for... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'epcr_threads'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'val... | def epcr_threads(self, formattedprimers, ampliconsize=10000):
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.epcr, args=())
threads.setDaemon(True)
threads.start()
logging.info('Running ePC... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'aggregate'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'};... | def aggregate(self):
for report in self.reportset:
printtime('Processing {}'.format(report.split('.')[0]), self.start)
header = '' if report != 'mlst.csv' else 'Strain,Genus,SequenceType,Matches,1,2,3,4,5,6,7\n'
data = ''
with open(os.path.join(self.reportpath, re... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_parse_sequences'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'valu... | def _parse_sequences(ilines, expect_qlen):
while True:
first = next(ilines)
if first.startswith('_') and first.endswith('].'):
break
try:
index, this_len, query_len = _parse_seq_preheader(first)
except ValueError:
logging.warn('Unparseable line (SK... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'realign_seqs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'va... | def realign_seqs(block, gap_char='.', align_indels=False):
all_chars = [list(sq['seq']) for sq in block['sequences']]
nrows = len(all_chars)
i = 0
while i < len(all_chars[0]):
rows_need_gaps = [r for r in all_chars if not r[i].islower()]
if len(rows_need_gaps) != nrows:
for r... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'collapse_to_consensus'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children'... | def collapse_to_consensus(seqrecords, strict=False, do_iron=True):
level = 0
name = seqrecords[0].id
if hasattr(seqrecords, '_records'):
if hasattr(seqrecords, 'level'):
level = seqrecords.level
if hasattr(seqrecords, 'name'):
name = seqrecords.name
seqrecords... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iron'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sequence'}; ... | def iron(sequence):
r_indel = re.compile(r'(-[a-y]|[a-y]-)')
orig_sequence = sequence
while r_indel.search(sequence):
in_insert = False
in_gap = False
seen_gaps = 0
inserts = []
outchars = []
for char in sequence:
if in_insert:
if c... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '4']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'collect_reponames'}; {'id': '3', 'type': 'parameters', 'children': []}; {'id': '4', 'type': 'block', 'children': ['5', '9', '146', '21... | def collect_reponames():
reponames = []
try:
with open(os.devnull) as devnull:
remote_data = subprocess.check_output(["git","remote","-v","show"],stderr=devnull)
branches = {}
for line in remote_data.decode('utf-8').split("\n"):
if line.strip() == "":
continue
remote_match = re_mote.match(line)
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'build_markdown_table'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': ... | def build_markdown_table(headers, rows, row_keys=None):
row_maxes = _find_row_maxes(headers, rows)
row_keys = row_keys or [key for key, value in headers.items()]
table = [
_build_row(headers, row_maxes, row_keys),
_build_separator(row_maxes, row_keys)
]
for row in rows:
table... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_publication_assistant'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children... | def create_publication_assistant(self, **args):
'''
Create an assistant for a dataset that allows to make PID
requests for the dataset and all of its files.
:param drs_id: Mandatory. The dataset id of the dataset
to be published.
:param version_number: Mandatory. The ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'replace_source'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'childre... | def replace_source(self, source, name, modules, prefix):
needs_windll = False
def _func_replacer(match, modules, windll):
matched = match.group(0)
if matched in self.BLACKLIST:
return matched
module = self.database.query_func_module(matched)
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_item'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def sort_item(iterable, number, reverse=False):
return sorted(iterable, key=itemgetter(number), reverse=reverse) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_equivalent_positions'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def get_equivalent_positions(block):
consensus = block['sequences'][0]['seq']
rest = block['sequences'][1:]
if '-' in consensus or '.' in consensus:
raise ValueError("First sequence (consensus?) contains gaps")
seen = set()
dupes = set()
for rec in rest:
if rec['id'] in seen:
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'remove_path_segments'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], '... | def remove_path_segments(segments, removes):
if segments == ['']:
segments.append('')
if removes == ['']:
removes.append('')
if segments == removes:
ret = []
elif len(removes) > len(segments):
ret = segments
else:
removes2 = list(removes)
if len(remove... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'error'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children... | def error(
cls,
template,
default_params={},
cause=None,
stack_depth=0,
**more_params
):
if not is_text(template):
sys.stderr.write(str("Log.error was expecting a unicode template"))
Log.error("Log.error was expecting a unicode template... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'summary_reporter'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def summary_reporter(self):
logging.info('Creating MOB-recon summary report')
with open(os.path.join(self.reportpath, 'mob_recon_summary.csv'), 'w') as summary:
data = 'Strain,Location,Contig,Incompatibility,IncompatibilityAccession,RelaxaseType,' \
'MashNearestNeighbor,Ma... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'amrsummary'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}... | def amrsummary(self):
logging.info('Creating AMR summary table from ResFinder and MOB-recon outputs')
with open(os.path.join(self.reportpath, 'amr_summary.csv'), 'w') as amr:
data = 'Strain,Gene,Allele,Resistance,PercentIdentity,Contig,Location,PlasmidIncompatibilitySets\n'
for s... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'geneseekrsummary'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def geneseekrsummary(self):
logging.info('Creating predicted plasmid-borne gene summary table')
with open(os.path.join(self.reportpath, 'plasmid_borne_summary.csv'), 'w') as pbs:
data = 'Strain,Gene,PercentIdentity,Contig,Location,PlasmidIncompatibilitySets\n'
for sample in self.... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filterunique'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self... | def filterunique(self):
for sample in self.metadata:
sample[self.analysistype].blastresults = list()
resultdict = dict()
rowdict = dict()
try:
for contig in sample[self.analysistype].queryranges:
for location in sample[self.anal... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'makedbthreads'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sel... | def makedbthreads(self):
for sample in self.metadata:
if sample[self.analysistype].combinedtargets != 'NA':
self.targetfolders.add(sample[self.analysistype].targetpath)
for i in range(len(self.targetfolders)):
threads = Thread(target=self.makeblastdb, args=())
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'cowbat'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'... | def cowbat(self):
logging.info('Beginning COWBAT database downloads')
if self.overwrite or not os.path.isdir(os.path.join(self.databasepath, 'genesippr')):
self.sipprverse_targets(databasepath=self.databasepath)
if self.overwrite or not os.path.isdir(os.path.join(self.databasepath, '... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'setCalibration'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [... | def setCalibration(self, dbBoostArray, frequencies, frange):
if dbBoostArray is not None and frequencies is not None:
logger = logging.getLogger('main')
if dbBoostArray.shape != frequencies.shape:
logger.error("ERROR: calibration array and frequency array must have same d... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'expandFunction'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def expandFunction(self, func, args=[]):
params = self._autoParams.allData()
steps = self.autoParamRanges()
ntraces = 1
for p in steps:
ntraces = ntraces*len(p)
varylist = [[None for x in range(len(params))] for y in range(ntraces)]
x = 1
for iset, ste... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'signal'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'... | def signal(self, force_fs=False):
assert None not in self.voltage_limits, 'Max voltage level not set'
if force_fs:
samplerate = force_fs
else:
samplerate = self.samplerate()
track_signals = []
max_db = max([comp.intensity() for t in self._segments for comp... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'verify'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'... | def verify(self, windowSize=None):
if self.samplerate() is None:
return "Multiple recording files with conflicting samplerates"
msg = self._autoParams.verify()
if msg:
return msg
if self.traceCount() == 0:
return "Test is empty"
if windowSize i... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'getLogicalLines'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def getLogicalLines(fp, allowQP=True, findBegin=False):
if not allowQP:
val = fp.read(-1)
lineNumber = 1
for match in logical_lines_re.finditer(val):
line, n = wrap_re.subn('', match.group())
if line != '':
yield line, lineNumber
lineNumber... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_bind_model'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'... | def _bind_model(self):
if self.groups[0].level != 0:
self.log.info("Got invalid first group: {0}".format(self.groups[0]))
raise ValueError("Invalid group tree: first group must have level of 0 (got {0})".format(self.groups[0].level))
class Stack(list):
def push(self, ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bowtie'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'... | def bowtie(self):
for i in range(self.cpus):
threads = Thread(target=self.align, args=())
threads.setDaemon(True)
threads.start()
with progressbar(self.metadata) as bar:
for sample in bar:
sample.mapping = GenObject()
sagen ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'validate_pages_json_data'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [... | def validate_pages_json_data(d, preferred_lang):
from .models import Page
errors = []
seen_complete_slugs = dict(
(lang[0], set()) for lang in settings.PAGE_LANGUAGES)
valid_templates = set(t[0] for t in settings.get_page_templates())
valid_templates.add(settings.PAGE_DEFAULT_TEMPLATE)
i... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'import_po_files'}; {'id': '3', 'type': 'parameters', 'children': ['4', '7']}; {'id': '4', 'type': 'default_parameter', 'children': ['... | def import_po_files(path='poexport', stdout=None):
import polib
from basic_cms.models import Page, Content
source_language = settings.PAGE_DEFAULT_LANGUAGE
source_list = []
pages_to_invalidate = []
for page in Page.objects.published():
source_list.extend(page.content_by_language(source_l... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_scene_suggestions'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def get_scene_suggestions(self, current):
l = []
if isinstance(current, djadapter.models.Asset):
l.append(current)
l.extend(list(current.assets.all()))
return l |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'assert_variable_type'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': ... | def assert_variable_type(variable, expected_type, raise_exception=True):
if not isinstance(expected_type, list):
expected_type = [expected_type]
for t in expected_type:
if not isinstance(t, type):
raise ValueError('expected_type argument "%s" is not a type' %str(t))
if not isinst... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id'... | def run(self):
while not self.stopped.isSet():
try:
timeout = (self._state != 'idle') and 0.2 or None
rdlist, _, _ = select.select([self._socket.fileno()], [], [], timeout)
if not rdlist:
if self._state != 'idle':
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_inc'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self... | def get_inc(self, native=False):
if self.sdk_version == 'v7.0A':
include = os.path.join(self.sdk_dir, 'include')
if os.path.isdir(include):
logging.info(_('using include: %s'), include)
return [include]
logging.debug(_('include not found: %s'),... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_lib'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value':... | def get_lib(self, arch='x86', native=False):
if self.sdk_version == 'v7.0A':
if arch == 'x86':
arch = ''
lib = os.path.join(self.sdk_dir, 'lib', arch)
if os.path.isdir(lib):
logging.info(_('using lib: %s'), lib)
return [lib]
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'interrogate'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children'... | def interrogate(self, platformIdentifier, configuration, libraries, libOverrides = {}):
libModules = list([lib for lib in libraries if lib not in libOverrides])
details = ThirdPartyLibraryDetails()
if len(libModules) > 0:
modules = self._getThirdPartyLibs(platformIdentifier, configuration)
modules = [m for ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_getThirdPartyLibs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': []... | def _getThirdPartyLibs(self, platformIdentifier, configuration):
cachedList = CachedDataManager.getCachedDataKey(self.engineVersionHash, 'ThirdPartyLibraries')
if cachedList != None:
return cachedList
tempDir = tempfile.mkdtemp()
jsonFile = os.path.join(tempDir, 'ubt_output.json')
sentinelFile = os.path.jo... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '57']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'add_vt'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27', '30', '33', '36', '3... | def add_vt(self, vt_id, name=None, vt_params=None, vt_refs=None,
custom=None, vt_creation_time=None, vt_modification_time=None,
vt_dependencies=None, summary=None, impact=None, affected=None,
insight=None, solution=None, solution_t=None, detection=None,
qod_t=... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_preprocess_scan_params'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': []... | def _preprocess_scan_params(self, xml_params):
params = {}
for param in xml_params:
params[param.tag] = param.text or ''
for key in self.scanner_params:
if key not in params:
params[key] = self.get_scanner_param_default(key)
if self.get_sca... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'start_scan'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def start_scan(self, scan_id, targets, parallel=1):
os.setsid()
multiscan_proc = []
logger.info("%s: Scan started.", scan_id)
target_list = targets
if target_list is None or not target_list:
raise OSPDError('Erroneous targets list', 'start_scan')
for index, ta... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ports_as_list'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'por... | def ports_as_list(port_str):
if not port_str:
LOGGER.info("Invalid port value")
return [None, None]
if ports_str_check_failed(port_str):
LOGGER.info("{0}: Port list malformed.")
return [None, None]
tcp_list = list()
udp_list = list()
ports = port_str.replace(' ', '')
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_args_parser'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value':... | def create_args_parser(description):
parser = argparse.ArgumentParser(description=description)
def network_port(string):
value = int(string)
if not 0 < value <= 65535:
raise argparse.ArgumentTypeError(
'port must be in ]0,65535] interval')
return value
def... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_handle_func'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children... | def _handle_func(self, value, rule, path, done=None):
func = rule.func
if not func:
return
found_method = False
for extension in self.loaded_extensions:
method = getattr(extension, func, None)
if method:
found_method = True
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_validate_range'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11']}; {'id': '4', 'type': 'id... | def _validate_range(self, max_, min_, max_ex, min_ex, value, path, prefix):
if not isinstance(value, int) and not isinstance(value, float):
raise CoreError("Value must be a integer type")
log.debug(
u"Validate range : %s : %s : %s : %s : %s : %s",
max_,
mi... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'tsses'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']}; {'id': '4', 'type': 'identifier', 'c... | def tsses(db, merge_overlapping=False, attrs=None, attrs_sep=":",
merge_kwargs=None, as_bed6=False, bedtools_227_or_later=True):
_override = os.environ.get('GFFUTILS_USES_BEDTOOLS_227_OR_LATER', None)
if _override is not None:
if _override == 'true':
bedtools_227_or_later = True
... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'interfeatures'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']}; {'id': '4', 'type': 'identifi... | def interfeatures(self, features, new_featuretype=None,
merge_attributes=True, dialect=None,
attribute_func=None, update_attributes=None):
for i, f in enumerate(features):
if i == 0:
interfeature_start = f.stop
last_feature ... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'update'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'val... | def update(self, data, make_backup=True, **kwargs):
from gffutils import create
from gffutils import iterators
if make_backup:
if isinstance(self.dbfn, six.string_types):
shutil.copy2(self.dbfn, self.dbfn + '.bak')
_iterator_kwargs = {}
for k, v in kwa... |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_introns'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier',... | def create_introns(self, exon_featuretype='exon',
grandparent_featuretype='gene', parent_featuretype=None,
new_featuretype='intron', merge_attributes=True):
if (grandparent_featuretype and parent_featuretype) or (
grandparent_featuretype is None and pare... |
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