sequence stringlengths 492 15.9k | code stringlengths 75 8.58k |
|---|---|
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:movefastq; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, string:'Moving... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 1, 11; 2, function_name:add_raw_entity; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, typed_parameter; 5, 6; 5, 7; 6, identifier:entity; 7, type; 7, 8; 8, identifier:dict; 9, type; 9, 10; 10, identifier:dict; 11, block; 11, 12; 11, 21; 11, 35; 11, 43; 11, 5... | def add_raw_entity(self, entity: dict) -> dict:
needed_in_entity = set([
'label',
'type',
])
options_in_entity = set([
'label',
'type',
'definition',
'comment',
'superclass',
'synonyms',
'... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 1, 19; 2, function_name:delete_annotation; 3, parameters; 3, 4; 3, 5; 3, 9; 3, 13; 4, identifier:self; 5, typed_parameter; 5, 6; 5, 7; 6, identifier:term_ilx_id; 7, type; 7, 8; 8, identifier:str; 9, typed_parameter; 9, 10; 9, 11; 10, identifier:annotation_type... | 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'
)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:configfilepopulator; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 18; 5, 30; 5, 88; 5, 124; 5, 140; 5, 148; 5, 320; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:self; 10, ide... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_check_time_format; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:labels; 6, identifier:values; 7, block; 7, 8; 8, for_statement; 8, 9; 8, 12; 8, 17; 9, pattern_list; 9, 10; 9, 11; 10, identifier:label; 11, identifier:value... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:readlength; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, string:'Estim... | 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.... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:confirm; 3, parameters; 3, 4; 3, 7; 3, 10; 3, 15; 3, 18; 4, default_parameter; 4, 5; 4, 6; 5, identifier:prompt; 6, string:'Really?'; 7, default_parameter; 7, 8; 7, 9; 8, identifier:color; 9, string:'warning'; 10, default_parameter; 10, 11; 10... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:from_string; 3, parameters; 3, 4; 3, 5; 4, identifier:cls; 5, identifier:action_str; 6, block; 6, 7; 6, 11; 6, 181; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:args; 10, dictionary; 11, try_statement; 11, 12; 11, 22... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:epcrparsethreads; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 11; 5, 53; 6, import_from_statement; 6, 7; 6, 9; 7, dotted_name; 7, 8; 8, identifier:Bio; 9, dotted_name; 9, 10; 10, identifier:SeqIO; 11, for_statement; 11, 12; 11, ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:trimquality; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 5, 392; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, stri... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:contamination_finder; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:input_path; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:report_path; 10, None; 11, block; 11, 12; 11, 19; ... | 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
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:subclass_genesis; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:genesisclass; 6, block; 6, 7; 6, 454; 6, 465; 7, class_definition; 7, 8; 7, 9; 7, 11; 8, identifier:MayaGenesisWin; 9, argument_list; 9, 10; 10, identifier:genesiscl... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 35; 1, 37; 2, function_name:override_options; 3, parameters; 3, 4; 3, 8; 3, 18; 3, 30; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:config; 6, type; 6, 7; 7, identifier:DictLike; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:selected_options; 10, type; 10, 11; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 24; 1, 36; 2, function_name:determine_selection_of_iterable_values_from_config; 3, parameters; 3, 4; 3, 8; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:config; 6, type; 6, 7; 7, identifier:DictLike; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:possible_iterable... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 1, 20; 2, function_name:create_key_index_object; 3, parameters; 3, 4; 3, 8; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:key_index_name; 6, type; 6, 7; 7, identifier:str; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:iterables; 10, type; 10, 11; 11, generic_... | 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"... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 34; 1, 50; 2, function_name:create_objects_from_iterables; 3, parameters; 3, 4; 3, 5; 3, 9; 3, 19; 3, 29; 4, identifier:obj; 5, typed_parameter; 5, 6; 5, 7; 6, identifier:args; 7, type; 7, 8; 8, identifier:dict; 9, typed_parameter; 9, 10; 9, 11; 10, identifier:ite... | 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(
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 42; 1, 58; 2, function_name:iterate_with_selected_objects_in_order; 3, parameters; 3, 4; 3, 14; 3, 28; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:analysis_objects; 6, type; 6, 7; 7, generic_type; 7, 8; 7, 9; 8, identifier:Mapping; 9, type_parameter; 9, 10; 9, 1... | 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):... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:phenotypes_to_scored; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:phenotypes; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:overwrite; 10, False; 11, block; 11, 12; 11, 25; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:subset; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:logic; 6, default_parameter; 6, 7; 6, 8; 7, identifier:update; 8, False; 9, block; 9, 10; 9, 16; 9, 22; 9, 30; 9, 34; 9, 40; 9, 52; 9, 66; 9, 165; 9, 174; 9, 227; 9, 235... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:collapse_phenotypes; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:input_phenotype_labels; 6, identifier:output_phenotype_label; 7, default_parameter; 7, 8; 7, 9; 8, identifier:verbose; 9, True; 10, block; 10, 11; 10... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:scored_to_phenotype; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:phenotypes; 6, block; 6, 7; 6, 85; 6, 93; 6, 114; 6, 145; 7, function_definition; 7, 8; 7, 9; 7, 12; 8, function_name:_apply_score; 9, parameters; 9, 10; 9, 11; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:spike_times; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:signal; 5, identifier:threshold; 6, identifier:fs; 7, default_parameter; 7, 8; 7, 9; 8, identifier:absval; 9, True; 10, block; 10, 11; 10, 15; 10, 27; 10, 39; 10, 56; 10, 297; 1... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:bin_spikes; 3, parameters; 3, 4; 3, 5; 4, identifier:spike_times; 5, identifier:binsz; 6, block; 6, 7; 6, 23; 6, 51; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:bins; 10, call; 10, 11; 10, 14; 11, attribute; 11, 12;... | 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 |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:corewriter; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 14; 5, 243; 5, 288; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 9; 8, identifier:printtime; 9, argument_list; 9, 10; 9, 11; 10, string:'Creating core allele files'; 11... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:profiler; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 14; 5, 43; 5, 62; 5, 66; 5, 148; 5, 184; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 9; 8, identifier:printtime; 9, argument_list; 9, 10; 9, 11; 10, string:'Calculating ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 23; 2, function_name:row2dict; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 4, identifier:row; 5, default_parameter; 5, 6; 5, 7; 6, identifier:depth; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:exclude; 10, None; 11, default_parameter... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 24; 2, function_name:dict2row; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 21; 4, identifier:d; 5, identifier:model; 6, default_parameter; 6, 7; 6, 8; 7, identifier:rel; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:exclude; 11, No... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 74; 1, 76; 2, function_name:remote; 3, parameters; 3, 4; 3, 13; 3, 14; 3, 17; 3, 20; 3, 23; 3, 26; 3, 29; 3, 32; 3, 42; 3, 45; 3, 55; 3, 65; 3, 68; 3, 71; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:cmd; 6, type; 6, 7; 7, call; 7, 8; 7, 9; 8, identifier:arg; 9, ... | 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,
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 69; 1, 71; 2, function_name:sync; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 10; 3, 13; 3, 16; 3, 22; 3, 25; 3, 28; 3, 31; 3, 34; 3, 37; 3, 40; 3, 43; 3, 53; 3, 63; 3, 66; 4, identifier:source; 5, identifier:destination; 6, identifier:host; 7, default_parameter; 7,... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 22; 1, 24; 2, function_name:_determine_outliers_for_moving_average; 3, parameters; 3, 4; 3, 10; 3, 14; 3, 18; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:moving_average; 6, type; 6, 7; 7, attribute; 7, 8; 7, 9; 8, identifier:np; 9, identifier:ndarray; 10, typed_... | 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) ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:make_dynamic_class; 3, parameters; 3, 4; 3, 5; 4, identifier:typename; 5, identifier:field_names; 6, block; 6, 7; 6, 28; 6, 36; 6, 44; 6, 65; 6, 71; 6, 77; 6, 83; 6, 100; 6, 106; 6, 120; 6, 156; 7, if_statement; 7, 8; 7, 13; 8, call; 8, 9; 8, 1... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:verifyInputs; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:mode; 6, block; 6, 7; 6, 34; 6, 431; 7, if_statement; 7, 8; 7, 16; 8, comparison_operator:<; 8, 9; 8, 15; 9, call; 9, 10; 9, 11; 10, identifier:len; 11, argument_list; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:complete; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:command_line; 5, identifier:current_token; 6, identifier:position; 7, typed_parameter; 7, 8; 7, 9; 8, identifier:shell; 9, type; 9, 10; 10, call; 10, 11; 10, 12; 11, identifier:arg... | 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)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:export; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:context; 5, identifier:keywords; 6, identifier:module; 7, identifier:update; 8, block; 8, 9; 8, 19; 8, 27; 8, 31; 8, 197; 9, expression_statement; 9, 10; 10, call; 10, 11; 10, 14; 11,... | 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]
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_source; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:label; 5, identifier:source_type; 6, dictionary_splat_pattern; 6, 7; 7, identifier:kwargs; 8, block; 8, 9; 8, 27; 8, 53; 9, if_statement; 9, 10; 9, 15; 10, comparison_operator:not; 10, ... | 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:... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 37; 1, 39; 2, function_name:_project_observable; 3, parameters; 3, 4; 3, 5; 3, 9; 3, 13; 3, 24; 3, 35; 4, identifier:self; 5, typed_parameter; 5, 6; 5, 7; 6, identifier:input_key; 7, type; 7, 8; 8, identifier:str; 9, typed_parameter; 9, 10; 9, 11; 10, identifier: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:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:getrruleset; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:addRDate; 7, False; 8, block; 8, 9; 8, 13; 8, 469; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:rrules... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 2, function_name:list_processed_parameter_group_histogram; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:group; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:start; 10, None; 11, ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:list_completeness_index; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:start; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:stop; 10, None; 11, block; 11, 12; 11, 16; 11, 30; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 20; 2, function_name:list_packets; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:name; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:start; 10, None; 11, default_parameter; 11,... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 26; 2, function_name:list_events; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 3, 23; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:source; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:severity; 10, None; 11, defa... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:list_parameter_ranges; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 4, identifier:self; 5, identifier:parameter; 6, default_parameter; 6, 7; 6, 8; 7, identifier:start; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:copy_file; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 4, identifier:source; 5, identifier:destination; 6, default_parameter; 6, 7; 6, 8; 7, identifier:unique; 8, False; 9, default_parameter; 9, 10; 9, 11; 10, identifier:sort; 11, Fal... | 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) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 2, function_name:tree; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 4, identifier:node; 5, default_parameter; 5, 6; 5, 7; 6, identifier:formatter; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:prefix; 10, None; 11, default_parameter; 11, 12; 11, ... | 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
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 2, function_name:run; 3, parameters; 4, block; 4, 5; 4, 11; 4, 20; 4, 26; 4, 35; 4, 44; 4, 81; 4, 87; 4, 99; 4, 136; 4, 148; 4, 163; 4, 175; 4, 177; 4, 195; 4, 206; 4, 220; 4, 224; 4, 240; 4, 290; 4, 314; 4, 346; 4, 350; 4, 384; 4, 388; 4, 404; 4, 429; 5, expre... | 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(... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:filter_seq; 3, parameters; 3, 4; 4, identifier:seq; 5, block; 5, 6; 5, 8; 5, 15; 5, 26; 5, 38; 5, 44; 5, 55; 5, 66; 5, 77; 5, 88; 5, 117; 5, 131; 5, 144; 6, expression_statement; 6, 7; 7, string:'''Examines unreserved sequences to see if they a... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:add_data; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:filenames; 6, block; 6, 7; 6, 56; 6, 119; 6, 170; 6, 211; 6, 352; 7, function_definition; 7, 8; 7, 9; 7, 11; 8, function_name:_parse_table; 9, parameters; 9, 10; 10, identif... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:check_tags; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:repos; 5, identifier:tags; 6, default_parameter; 6, 7; 6, 8; 7, identifier:ignore_existing; 8, False; 9, default_parameter; 9, 10; 9, 11; 10, identifier:fail_fast; 11, False; 12,... | 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 =... |
0, module; 0, 1; 0, 42; 0, 44; 0, 46; 0, 48; 0, 50; 0, 52; 0, 54; 0, 56; 0, 58; 0, 61; 0, 82; 1, function_definition; 1, 2; 1, 3; 1, 8; 1, 37; 1, 39; 2, function_name:getmlsthelper; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:referencefilepath; 5, identifier:start; 6, identifier:organism; 7, identifier:update;... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:set; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, dictionary_splat_pattern; 5, 6; 6, identifier:kwargs; 7, block; 7, 8; 7, 16; 7, 32; 7, 56; 7, 115; 7, 131; 7, 139; 7, 152; 7, 165; 7, 178; 7, 191; 7, 204; 7, 217; 7, 230; 7, 245; 7, 258; 7,... | 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:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:readlist; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 14; 5, 50; 5, 67; 5, 75; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 9; 8, identifier:printtime; 9, argument_list; 9, 10; 9, 11; 10, string:'Sorting reads'; 11, attribut... | 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)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:has_change_permission; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:page; 6, identifier:lang; 7, default_parameter; 7, 8; 7, 9; 8, identifier:method; 9, None; 10, block; 10, 11; 10, 18; 10, 27; 10, 72; 10, 80; 10, 1... | 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:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:args; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 12; 5, 18; 5, 29; 5, 35; 5, 41; 5, 47; 5, 53; 5, 59; 5, 70; 5, 76; 5, 107; 5, 326; 5, 332; 5, 363; 5, 418; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:epcr_threads; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:formattedprimers; 6, default_parameter; 6, 7; 6, 8; 7, identifier:ampliconsize; 8, integer:10000; 9, block; 9, 10; 9, 52; 9, 59; 9, 294; 10, for_statement; 10, 11;... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:aggregate; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, for_statement; 6, 7; 6, 8; 6, 11; 7, identifier:report; 8, attribute; 8, 9; 8, 10; 9, identifier:self; 10, identifier:reportset; 11, block; 11, 12; 11, 32; 11, 41; 11, 45; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_parse_sequences; 3, parameters; 3, 4; 3, 5; 4, identifier:ilines; 5, identifier:expect_qlen; 6, block; 6, 7; 7, while_statement; 7, 8; 7, 9; 8, True; 9, block; 9, 10; 9, 17; 9, 33; 9, 57; 9, 74; 9, 101; 9, 116; 9, 127; 9, 138; 9, 174; 9, 210; ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:realign_seqs; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:block; 5, default_parameter; 5, 6; 5, 7; 6, identifier:gap_char; 7, string:'.'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:align_indels; 10, False; 11, block; 11, 12; 11, 27; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:collapse_to_consensus; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:seqrecords; 5, default_parameter; 5, 6; 5, 7; 6, identifier:strict; 7, False; 8, default_parameter; 8, 9; 8, 10; 9, identifier:do_iron; 10, True; 11, block; 11, 12; 11, 16; ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:iron; 3, parameters; 3, 4; 4, identifier:sequence; 5, block; 5, 6; 5, 15; 5, 19; 5, 389; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:r_indel; 9, call; 9, 10; 9, 13; 10, attribute; 10, 11; 10, 12; 11, identifier:re; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 2, function_name:collect_reponames; 3, parameters; 4, block; 4, 5; 4, 9; 4, 146; 4, 216; 5, expression_statement; 5, 6; 6, assignment; 6, 7; 6, 8; 7, identifier:reponames; 8, list:[]; 9, try_statement; 9, 10; 9, 136; 9, 140; 10, block; 10, 11; 10, 40; 10, 44; 1... | 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)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:build_markdown_table; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:headers; 5, identifier:rows; 6, default_parameter; 6, 7; 6, 8; 7, identifier:row_keys; 8, None; 9, block; 9, 10; 9, 18; 9, 34; 9, 49; 9, 65; 10, expression_statement; 10, 11; ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:create_publication_assistant; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, dictionary_splat_pattern; 5, 6; 6, identifier:args; 7, block; 7, 8; 7, 10; 7, 16; 7, 23; 7, 33; 7, 59; 7, 85; 7, 95; 7, 147; 7, 153; 8, expression_statement; 8, 9; ... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:replace_source; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:self; 5, identifier:source; 6, identifier:name; 7, identifier:modules; 8, identifier:prefix; 9, block; 9, 10; 9, 14; 9, 102; 9, 115; 9, 126; 9, 135; 9, 139; 9, 196; 9, 2... | 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)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:sort_item; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:iterable; 5, identifier:number; 6, default_parameter; 6, 7; 6, 8; 7, identifier:reverse; 8, False; 9, block; 9, 10; 10, return_statement; 10, 11; 11, call; 11, 12; 11, 13; 12, identifier... | def sort_item(iterable, number, reverse=False):
return sorted(iterable, key=itemgetter(number), reverse=reverse) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_equivalent_positions; 3, parameters; 3, 4; 4, identifier:block; 5, block; 5, 6; 5, 16; 5, 26; 5, 40; 5, 46; 5, 52; 5, 83; 5, 98; 5, 102; 5, 106; 5, 128; 5, 148; 5, 265; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier... | 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:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:remove_path_segments; 3, parameters; 3, 4; 3, 5; 4, identifier:segments; 5, identifier:removes; 6, block; 6, 7; 6, 20; 6, 33; 6, 142; 7, if_statement; 7, 8; 7, 12; 8, comparison_operator:==; 8, 9; 8, 10; 9, identifier:segments; 10, list:['']; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 2, function_name:error; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 4, identifier:cls; 5, identifier:template; 6, default_parameter; 6, 7; 6, 8; 7, identifier:default_params; 8, dictionary; 9, default_parameter; 9, 10; 9, 11; 10, identifier:cause; 11,... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:summary_reporter; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, string:... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:amrsummary; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, string:'Creat... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:geneseekrsummary; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:logging; 10, identifier:info; 11, argument_list; 11, 12; 12, string:... | 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.... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:filterunique; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, for_statement; 6, 7; 6, 8; 6, 11; 7, identifier:sample; 8, attribute; 8, 9; 8, 10; 9, identifier:self; 10, identifier:metadata; 11, block; 11, 12; 11, 24; 11, 30; 11, 36;... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:makedbthreads; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 38; 5, 77; 5, 164; 6, for_statement; 6, 7; 6, 8; 6, 11; 7, identifier:sample; 8, attribute; 8, 9; 8, 10; 9, identifier:self; 10, identifier:metadata; 11, block; 11, 12; ... | 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=())
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:cowbat; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 5, 49; 5, 85; 5, 116; 5, 152; 5, 188; 5, 229; 5, 265; 5, 307; 5, 349; 5, 391; 5, 433; 5, 469; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10... | 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, '... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:setCalibration; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:dbBoostArray; 6, identifier:frequencies; 7, identifier:frange; 8, block; 8, 9; 9, if_statement; 9, 10; 9, 17; 9, 189; 10, boolean_operator:and; 10, 11; 10,... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:expandFunction; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:func; 6, default_parameter; 6, 7; 6, 8; 7, identifier:args; 8, list:[]; 9, block; 9, 10; 9, 20; 9, 28; 9, 32; 9, 45; 9, 66; 9, 70; 9, 117; 9, 121; 9, 187; 9, 216... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:signal; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:force_fs; 7, False; 8, block; 8, 9; 8, 16; 8, 33; 8, 37; 8, 57; 8, 61; 8, 122; 8, 135; 8, 145; 8, 161; 8, 182; 8, 194; 8, 252; 8, 259; 8, 263... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:verify; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:windowSize; 7, None; 8, block; 8, 9; 8, 20; 8, 30; 8, 35; 8, 46; 8, 78; 8, 91; 8, 96; 8, 111; 8, 120; 9, if_statement; 9, 10; 9, 17; 10, comp... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:getLogicalLines; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:fp; 5, default_parameter; 5, 6; 5, 7; 6, identifier:allowQP; 7, True; 8, default_parameter; 8, 9; 8, 10; 9, identifier:findBegin; 10, False; 11, block; 11, 12; 12, if_statement; 1... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_bind_model; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 51; 5, 69; 5, 79; 5, 85; 5, 89; 5, 178; 6, if_statement; 6, 7; 6, 16; 7, comparison_operator:!=; 7, 8; 7, 15; 8, attribute; 8, 9; 8, 14; 9, subscript; 9, 10; 9, 13; 10, at... | 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, ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:bowtie; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 42; 5, 460; 6, for_statement; 6, 7; 6, 8; 6, 14; 7, identifier:i; 8, call; 8, 9; 8, 10; 9, identifier:range; 10, argument_list; 10, 11; 11, attribute; 11, 12; 11, 13; 12, ident... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:validate_pages_json_data; 3, parameters; 3, 4; 3, 5; 4, identifier:d; 5, identifier:preferred_lang; 6, block; 6, 7; 6, 14; 6, 18; 6, 36; 6, 52; 6, 61; 6, 83; 6, 89; 6, 370; 7, import_from_statement; 7, 8; 7, 12; 8, relative_import; 8, 9; 8, 10;... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:import_po_files; 3, parameters; 3, 4; 3, 7; 4, default_parameter; 4, 5; 4, 6; 5, identifier:path; 6, string:'poexport'; 7, default_parameter; 7, 8; 7, 9; 8, identifier:stdout; 9, None; 10, block; 10, 11; 10, 14; 10, 22; 10, 28; 10, 32; 10, 36;... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:get_scene_suggestions; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:current; 6, block; 6, 7; 6, 11; 6, 29; 6, 45; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:l; 10, list:[]; 11, if_statement; 11, 12;... | def get_scene_suggestions(self, current):
l = []
if isinstance(current, djadapter.models.Asset):
l.append(current)
l.extend(list(current.assets.all()))
return l |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:assert_variable_type; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:variable; 5, identifier:expected_type; 6, default_parameter; 6, 7; 6, 8; 7, identifier:raise_exception; 8, True; 9, block; 9, 10; 9, 23; 9, 45; 9, 63; 9, 125; 10, if_statement... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:run; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, while_statement; 6, 7; 6, 15; 7, not_operator; 7, 8; 8, call; 8, 9; 8, 14; 9, attribute; 9, 10; 9, 13; 10, attribute; 10, 11; 10, 12; 11, identifier:self; 12, identifier:stopped; ... | 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':
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_inc; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:native; 7, False; 8, block; 8, 9; 8, 67; 8, 167; 8, 256; 8, 267; 9, if_statement; 9, 10; 9, 15; 10, comparison_operator:==; 10, 11; 10, 14; ... | 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'),... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:get_lib; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:arch; 7, string:'x86'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:native; 10, False; 11, block; 11, 12; 11, 80; 11, 169; 11, 25... | 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]
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:interrogate; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:self; 5, identifier:platformIdentifier; 6, identifier:configuration; 7, identifier:libraries; 8, default_parameter; 8, 9; 8, 10; 9, identifier:libOverrides; 10, dictionary... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_getThirdPartyLibs; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:platformIdentifier; 6, identifier:configuration; 7, block; 7, 8; 7, 20; 7, 27; 7, 35; 7, 47; 7, 63; 7, 69; 7, 92; 7, 105; 7, 154; 7, 168; 7, 182; 7, 198; 7, ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 57; 2, function_name:add_vt; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 21; 3, 24; 3, 27; 3, 30; 3, 33; 3, 36; 3, 39; 3, 42; 3, 45; 3, 48; 3, 51; 3, 54; 4, identifier:self; 5, identifier:vt_id; 6, default_parameter; 6, 7; 6, 8; 7, identifier:na... | 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=... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_preprocess_scan_params; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:xml_params; 6, block; 6, 7; 6, 11; 6, 27; 6, 74; 6, 201; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:params; 10, dictionary; 11, ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:start_scan; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:scan_id; 6, identifier:targets; 7, default_parameter; 7, 8; 7, 9; 8, identifier:parallel; 9, integer:1; 10, block; 10, 11; 10, 17; 10, 21; 10, 29; 10, 33; 10,... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:ports_as_list; 3, parameters; 3, 4; 4, identifier:port_str; 5, block; 5, 6; 5, 21; 5, 38; 5, 44; 5, 50; 5, 60; 5, 69; 5, 78; 5, 103; 5, 128; 5, 135; 5, 139; 5, 143; 5, 248; 5, 293; 5, 338; 6, if_statement; 6, 7; 6, 9; 7, not_operator; 7, 8; 8, ... | 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(' ', '')
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:create_args_parser; 3, parameters; 3, 4; 4, identifier:description; 5, block; 5, 6; 5, 17; 5, 45; 5, 174; 5, 209; 5, 236; 5, 258; 5, 277; 5, 288; 5, 307; 5, 326; 5, 344; 5, 361; 5, 374; 5, 388; 5, 401; 6, expression_statement; 6, 7; 7, assignme... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:_handle_func; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:self; 5, identifier:value; 6, identifier:rule; 7, identifier:path; 8, default_parameter; 8, 9; 8, 10; 9, identifier:done; 10, None; 11, block; 11, 12; 11, 18; 11, 23; 11,... | 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
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:_validate_range; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 4, identifier:self; 5, identifier:max_; 6, identifier:min_; 7, identifier:max_ex; 8, identifier:min_ex; 9, identifier:value; 10, identifier:path; 11, identifier:... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 23; 2, function_name:tsses; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 4, identifier:db; 5, default_parameter; 5, 6; 5, 7; 6, identifier:merge_overlapping; 7, False; 8, default_parameter; 8, 9; 8, 10; 9, identifier:attrs; 10, None; 11, default_pa... | 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
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:interfeatures; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 4, identifier:self; 5, identifier:features; 6, default_parameter; 6, 7; 6, 8; 7, identifier:new_featuretype; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier... | 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 ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:update; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:self; 5, identifier:data; 6, default_parameter; 6, 7; 6, 8; 7, identifier:make_backup; 8, True; 9, dictionary_splat_pattern; 9, 10; 10, identifier:kwargs; 11, block; 11, 12; 11, 17; ... | 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... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 20; 2, function_name:create_introns; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:exon_featuretype; 7, string:'exon'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:grandparent_featuret... | 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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