nodes stringlengths 501 22.4k | edges stringlengths 138 5.07k | code stringlengths 108 19.3k |
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0, module; 1, function_definition; 2, function_name:gather_categories; 3, parameters; 4, block; 5, identifier:imap; 6, identifier:header; 7, default_parameter; 8, expression_statement; 9, comment:# If no categories provided, return all SampleIDs; 10, if_statement; 11, expression_statement; 12, expression_statement; 13,... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 4, 18; 4, 19; 4, 20; 4, 21; 4, 22; 4, 23; 4, 24; 4, 25; 4, 26; 7, 27; 7, 28; 8, 29; 10, 30; 10, 31; 11, 32; 12, 33; 13, 34; 14, 35; 14, 36; 14, 37; 16, 38; 16, 39; 18, 40; 18, 41; 20, 42; 21, 43; 21, 44; 21, 45... | def gather_categories(imap, header, categories=None):
"""
Find the user specified categories in the map and create a dictionary to contain the
relevant data for each type within the categories. Multiple categories will have their
types combined such that each possible combination will have its own entry... |
0, module; 1, function_definition; 2, function_name:sort_sam; 3, parameters; 4, block; 5, identifier:sam; 6, identifier:sort; 7, expression_statement; 8, expression_statement; 9, if_statement; 10, return_statement; 11, comment:"""
sort sam file
"""; 12, assignment; 13, comparison_operator:sort is True; 14, bloc... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 4, 9; 4, 10; 7, 11; 8, 12; 9, 13; 9, 14; 9, 15; 10, 16; 12, 17; 12, 18; 13, 19; 13, 20; 14, 21; 14, 22; 14, 23; 15, 24; 18, 25; 18, 26; 21, 27; 22, 28; 22, 29; 22, 30; 23, 31; 24, 32; 25, 33; 26, 34; 27, 35; 27, 36; 28, 37; 28, 38; 29, 39; 30, 40; 31, 41; 31, 42; 32, 43; ... | def sort_sam(sam, sort):
"""
sort sam file
"""
tempdir = '%s/' % (os.path.abspath(sam).rsplit('/', 1)[0])
if sort is True:
mapping = '%s.sorted.sam' % (sam.rsplit('.', 1)[0])
if sam != '-':
if os.path.exists(mapping) is False:
os.system("\
... |
0, module; 1, function_definition; 2, function_name:top_hits; 3, parameters; 4, block; 5, identifier:hits; 6, identifier:num; 7, identifier:column; 8, identifier:reverse; 9, expression_statement; 10, expression_statement; 11, for_statement; 12, comment:"""
get top hits after sorting by column number
"""; 13, ca... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 9, 12; 10, 13; 11, 14; 11, 15; 11, 16; 13, 17; 13, 18; 15, 19; 15, 20; 16, 21; 17, 22; 17, 23; 18, 24; 18, 25; 20, 26; 20, 27; 21, 28; 24, 29; 24, 30; 25, 31; 25, 32; 28, 33; 30, 34; 30, 35; 35, 36 | def top_hits(hits, num, column, reverse):
"""
get top hits after sorting by column number
"""
hits.sort(key = itemgetter(column), reverse = reverse)
for hit in hits[0:num]:
yield hit |
0, module; 1, function_definition; 2, function_name:numBlast_sort; 3, parameters; 4, block; 5, identifier:blast; 6, identifier:numHits; 7, identifier:evalueT; 8, identifier:bitT; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, expression_statement; 13, for_statement; 14, expression_stat... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 9, 16; 10, 17; 11, 18; 12, 19; 13, 20; 13, 21; 13, 22; 14, 23; 15, 24; 15, 25; 15, 26; 17, 27; 17, 28; 18, 29; 19, 30; 19, 31; 22, 32; 22, 33; 22, 34; 22, 35; 22, 36; 22, 37; 22, 38; 22, 39; 23, 40; 23, 41; 24, 42; 24, 43; 2... | def numBlast_sort(blast, numHits, evalueT, bitT):
"""
parse b6 output with sorting
"""
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
hmm = {h:[] for h in header}
for line in blast:
... |
0, module; 1, function_definition; 2, function_name:numDomtblout; 3, parameters; 4, block; 5, identifier:domtblout; 6, identifier:numHits; 7, identifier:evalueT; 8, identifier:bitT; 9, identifier:sort; 10, expression_statement; 11, if_statement; 12, expression_statement; 13, expression_statement; 14, expression_stateme... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 10, 17; 11, 18; 11, 19; 12, 20; 13, 21; 14, 22; 15, 23; 15, 24; 15, 25; 16, 26; 16, 27; 16, 28; 18, 29; 18, 30; 19, 31; 19, 32; 20, 33; 20, 34; 21, 35; 22, 36; 22, 37; 25, 38; 25, 39; 25, 40; 25, 41; 25, 42; 25, 43; 2... | def numDomtblout(domtblout, numHits, evalueT, bitT, sort):
"""
parse hmm domain table output
this version is faster but does not work unless the table is sorted
"""
if sort is True:
for hit in numDomtblout_sort(domtblout, numHits, evalueT, bitT):
yield hit
return
head... |
0, module; 1, function_definition; 2, function_name:S; 3, parameters; 4, block; 5, identifier:Document; 6, list_splat_pattern; 7, expression_statement; 8, expression_statement; 9, for_statement; 10, return_statement; 11, identifier:fields; 12, comment:"""Generate a MongoDB sort order list using the Django ORM style."""... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 4, 9; 4, 10; 6, 11; 7, 12; 8, 13; 9, 14; 9, 15; 9, 16; 10, 17; 13, 18; 13, 19; 16, 20; 16, 21; 16, 22; 16, 23; 16, 24; 16, 25; 16, 26; 20, 27; 20, 28; 20, 29; 21, 30; 22, 31; 22, 32; 23, 33; 23, 34; 24, 35; 24, 36; 25, 37; 26, 38; 27, 39; 27, 40; 29, 41; 29, 42; 29, 43; 3... | def S(Document, *fields):
"""Generate a MongoDB sort order list using the Django ORM style."""
result = []
for field in fields:
if isinstance(field, tuple): # Unpack existing tuple.
field, direction = field
result.append((field, direction))
continue
direction = ASCENDING
if not field.starts... |
0, module; 1, function_definition; 2, function_name:arrayuniqify; 3, parameters; 4, block; 5, identifier:X; 6, default_parameter; 7, expression_statement; 8, expression_statement; 9, expression_statement; 10, expression_statement; 11, if_statement; 12, identifier:retainorder; 13, False; 14, comment:"""
Very fast un... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 6, 12; 6, 13; 7, 14; 8, 15; 9, 16; 10, 17; 11, 18; 11, 19; 11, 20; 15, 21; 15, 22; 16, 23; 16, 24; 17, 25; 17, 26; 19, 27; 19, 28; 19, 29; 19, 30; 20, 31; 22, 32; 22, 33; 24, 34; 24, 35; 26, 36; 26, 37; 27, 38; 28, 39; 29, 40; 30, 41; 31, 42; 32, 43; 3... | def arrayuniqify(X, retainorder=False):
"""
Very fast uniqify routine for numpy arrays.
**Parameters**
**X** : numpy array
Determine the unique elements of this numpy array.
**retainorder** : Boolean, optional
Whether or not to return in... |
0, module; 1, function_definition; 2, function_name:equalspairs; 3, parameters; 4, block; 5, identifier:X; 6, identifier:Y; 7, expression_statement; 8, expression_statement; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, expression_statement; 13, expression_statement; 14, expression_st... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 7, 18; 8, 19; 9, 20; 10, 21; 11, 22; 12, 23; 13, 24; 14, 25; 15, 26; 16, 27; 17, 28; 19, 29; 19, 30; 20, 31; 20, 32; 21, 33; 21, 34; 22, 35; 22, 36; 23, 37; 23, 38; 24, 39; 24, 40; 25, 41; 25, 42; 26, 43; 26, 4... | def equalspairs(X, Y):
"""
Indices of elements in a sorted numpy array equal to those in another.
Given numpy array `X` and sorted numpy array `Y`, determine the indices in
Y equal to indices in X.
Returns `[A,B]` where `A` and `B` are numpy arrays of indices in `X` such
that::
... |
0, module; 1, function_definition; 2, function_name:_inplace_sort_by_id; 3, parameters; 4, block; 5, identifier:unsorted_list; 6, expression_statement; 7, if_statement; 8, expression_statement; 9, expression_statement; 10, delete_statement; 11, expression_statement; 12, comment:"""Takes a list of dicts each of which ha... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 6, 12; 7, 13; 7, 14; 8, 15; 9, 16; 10, 17; 11, 18; 13, 19; 14, 20; 15, 21; 15, 22; 16, 23; 16, 24; 17, 25; 17, 26; 18, 27; 18, 28; 19, 29; 19, 30; 22, 31; 22, 32; 23, 33; 23, 34; 27, 35; 27, 36; 28, 37; 30, 38; 30, 39; 31, 40; 31, 41; 32, 42; 32, 43; 3... | def _inplace_sort_by_id(unsorted_list):
"""Takes a list of dicts each of which has an '@id' key,
sorts the elements in the list by the value of the @id key.
Assumes that @id is unique or the dicts have a meaningul < operator
"""
if not isinstance(unsorted_list, list):
return
sorted_list ... |
0, module; 1, function_definition; 2, function_name:get_schemaloc_string; 3, parameters; 4, block; 5, identifier:self; 6, default_parameter; 7, default_parameter; 8, default_parameter; 9, expression_statement; 10, if_statement; 11, if_statement; 12, expression_statement; 13, for_statement; 14, if_statement; 15, return_... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 6, 16; 6, 17; 7, 18; 7, 19; 8, 20; 8, 21; 9, 22; 10, 23; 10, 24; 11, 25; 11, 26; 12, 27; 13, 28; 13, 29; 13, 30; 14, 31; 14, 32; 15, 33; 23, 34; 24, 35; 26, 36; 27, 37; 27, 38; 30, 39; 30, 40; 31, 41; 32, 42; 33, 43; 33, 44;... | def get_schemaloc_string(self, ns_uris=None, sort=False, delim="\n"):
"""Constructs and returns a schemalocation attribute. If no
namespaces in this set have any schema locations defined, returns
an empty string.
Args:
ns_uris (iterable): The namespaces to include in the co... |
0, module; 1, function_definition; 2, function_name:aggregate; 3, parameters; 4, block; 5, identifier:self; 6, default_parameter; 7, default_parameter; 8, default_parameter; 9, default_parameter; 10, default_parameter; 11, default_parameter; 12, default_parameter; 13, expression_statement; 14, if_statement; 15, express... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 3, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 6, 18; 6, 19; 7, 20; 7, 21; 8, 22; 8, 23; 9, 24; 9, 25; 10, 26; 10, 27; 11, 28; 11, 29; 12, 30; 12, 31; 13, 32; 14, 33; 14, 34; 14, 35; 15, 36; 16, 37; 17, 38; 17, 39; 17, 40; 34, 41; 35, 42; 36, 43; 36, 44; 37... | def aggregate(self, On=None, AggFuncDict=None, AggFunc=None, AggList =
None, returnsort=False,KeepOthers=True, keyfuncdict=None):
"""
Aggregate a tabarray on columns for given functions.
Method wraps::
tabular.spreadsheet.aggregate(self, On, AggFuncDict, AggFu... |
0, module; 1, function_definition; 2, function_name:argsort; 3, parameters; 4, block; 5, identifier:self; 6, default_parameter; 7, default_parameter; 8, default_parameter; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, return_statement; 13, identifier:axis; 14, unary_operator; 15, iden... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 4, 12; 6, 13; 6, 14; 7, 15; 7, 16; 8, 17; 8, 18; 9, 19; 10, 20; 11, 21; 12, 22; 14, 23; 16, 24; 20, 25; 20, 26; 21, 27; 21, 28; 26, 29; 26, 30; 28, 31; 28, 32; 29, 33; 29, 34; 30, 35; 30, 36; 30, 37; 30, 38; 30, 39; 31, 40; 31, 41; 32, 42; 33, 43; 33, ... | def argsort(self, axis=-1, kind='quicksort', order=None):
"""
Returns the indices that would sort an array.
.. note::
This method wraps `numpy.argsort`. This documentation is
modified from that of `numpy.argsort`.
Perform an indirect sort along the gi... |
0, module; 1, function_definition; 2, function_name:blt; 3, parameters; 4, type; 5, block; 6, typed_parameter; 7, typed_parameter; 8, generic_type; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, return_statement; 13, identifier:f; 14, type; 15, identifier:x; 16, type; 17, identifier:Di... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 4, 8; 5, 9; 5, 10; 5, 11; 5, 12; 6, 13; 6, 14; 7, 15; 7, 16; 8, 17; 8, 18; 9, 19; 10, 20; 11, 21; 12, 22; 14, 23; 16, 24; 18, 25; 18, 26; 20, 27; 20, 28; 21, 29; 21, 30; 22, 31; 22, 32; 22, 33; 22, 34; 22, 35; 22, 36; 22, 37; 22, 38; 23, 39; 23, 40; 24, 41; 24, 42; 25, 43; 26, ... | def blt(f: List[SYM], x: List[SYM]) -> Dict[str, Any]:
"""
Sort equations by dependence
"""
J = ca.jacobian(f, x)
nblock, rowperm, colperm, rowblock, colblock, coarserow, coarsecol = J.sparsity().btf()
return {
'J': J,
'nblock': nblock,
'rowperm': rowperm,
'colper... |
0, module; 1, function_definition; 2, function_name:sort_generators; 3, parameters; 4, block; 5, identifier:self; 6, expression_statement; 7, expression_statement; 8, comment:""" Reorders the list of generators according to bus index.
"""; 9, call; 10, attribute; 11, argument_list; 12, attribute; 13, identifier... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 6, 8; 7, 9; 9, 10; 9, 11; 10, 12; 10, 13; 11, 14; 12, 15; 12, 16; 14, 17; 14, 18; 18, 19; 18, 20; 19, 21; 20, 22; 20, 23; 22, 24; 22, 25 | def sort_generators(self):
""" Reorders the list of generators according to bus index.
"""
self.generators.sort(key=lambda gn: gn.bus._i) |
0, module; 1, function_definition; 2, function_name:list; 3, parameters; 4, comment:# pylint: disable=redefined-builtin; 5, block; 6, identifier:self; 7, default_parameter; 8, default_parameter; 9, default_parameter; 10, default_parameter; 11, default_parameter; 12, expression_statement; 13, expression_statement; 14, e... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 5, 12; 5, 13; 5, 14; 5, 15; 5, 16; 7, 17; 7, 18; 8, 19; 8, 20; 9, 21; 9, 22; 10, 23; 10, 24; 11, 25; 11, 26; 12, 27; 13, 28; 14, 29; 15, 30; 16, 31; 28, 32; 28, 33; 29, 34; 29, 35; 30, 36; 30, 37; 31, 38; 31, 39; 33, 40; 33, 41; 35, 42; 35, 43; 36, 44;... | def list(self, filter=None, type=None, sort=None, limit=None, page=None): # pylint: disable=redefined-builtin
"""Get a list of configs.
:param filter: (optional) Filters to apply as a string list.
:param type: (optional) `union` or `inter` as string.
:param sort: (optional) Sort fields ... |
0, module; 1, function_definition; 2, function_name:list_csv; 3, parameters; 4, comment:# pylint: disable=redefined-builtin; 5, block; 6, identifier:self; 7, default_parameter; 8, default_parameter; 9, default_parameter; 10, default_parameter; 11, default_parameter; 12, expression_statement; 13, return_statement; 14, i... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 5, 12; 5, 13; 7, 14; 7, 15; 8, 16; 8, 17; 9, 18; 9, 19; 10, 20; 10, 21; 11, 22; 11, 23; 12, 24; 13, 25; 25, 26; 25, 27; 26, 28; 26, 29; 28, 30; 28, 31; 29, 32; 29, 33; 29, 34; 29, 35; 29, 36; 29, 37; 29, 38; 30, 39; 30, 40; 32, 41; 32, 42; 38, 43; 38, ... | def list_csv(self, filter=None, type=None, sort=None, limit=None, page=None): # pylint: disable=redefined-builtin
"""Get a list of results as CSV.
:param filter: (optional) Filters to apply as a string list.
:param type: (optional) `union` or `inter` as string.
:param sort: (optional) S... |
0, module; 1, function_definition; 2, function_name:list_logdir; 3, parameters; 4, comment:# pylint: disable=invalid-name,redefined-builtin; 5, block; 6, identifier:self; 7, identifier:id; 8, default_parameter; 9, default_parameter; 10, expression_statement; 11, expression_statement; 12, expression_statement; 13, retur... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 3, 8; 3, 9; 5, 10; 5, 11; 5, 12; 5, 13; 8, 14; 8, 15; 9, 16; 9, 17; 10, 18; 11, 19; 12, 20; 13, 21; 19, 22; 19, 23; 20, 24; 20, 25; 21, 26; 21, 27; 23, 28; 23, 29; 25, 30; 25, 31; 26, 32; 26, 33; 27, 34; 27, 35; 27, 36; 30, 37; 30, 38; 31, 39; 31, 40; 31, 41; 32, 42; 32, 43; 36... | def list_logdir(self, id, filter=None, sort=None): # pylint: disable=invalid-name,redefined-builtin
"""Get a list of logdir files.
:param id: Result ID as an int.
:param filter: Filter to apply as string.
:param sort: Sort field to apply as string.
:return: :class:`results.LogDi... |
0, module; 1, function_definition; 2, function_name:list; 3, parameters; 4, comment:# pylint: disable=redefined-builtin; 5, block; 6, identifier:self; 7, default_parameter; 8, default_parameter; 9, default_parameter; 10, default_parameter; 11, default_parameter; 12, expression_statement; 13, expression_statement; 14, e... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 5, 12; 5, 13; 5, 14; 5, 15; 5, 16; 7, 17; 7, 18; 8, 19; 8, 20; 9, 21; 9, 22; 10, 23; 10, 24; 11, 25; 11, 26; 12, 27; 13, 28; 14, 29; 15, 30; 16, 31; 28, 32; 28, 33; 29, 34; 29, 35; 30, 36; 30, 37; 31, 38; 31, 39; 33, 40; 33, 41; 35, 42; 35, 43; 36, 44;... | def list(self, filter=None, type=None, sort=None, limit=None, page=None): # pylint: disable=redefined-builtin
"""Get a list of packages.
:param filter: (optional) Filters to apply as a string list.
:param type: (optional) `union` or `inter` as string.
:param sort: (optional) Sort fields... |
0, module; 1, function_definition; 2, function_name:list; 3, parameters; 4, comment:# pylint: disable=invalid-name,redefined-builtin; 5, block; 6, identifier:self; 7, identifier:id; 8, default_parameter; 9, default_parameter; 10, default_parameter; 11, default_parameter; 12, default_parameter; 13, expression_statement;... | 0, 1; 1, 2; 1, 3; 1, 4; 1, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 3, 12; 5, 13; 5, 14; 5, 15; 5, 16; 5, 17; 8, 18; 8, 19; 9, 20; 9, 21; 10, 22; 10, 23; 11, 24; 11, 25; 12, 26; 12, 27; 13, 28; 14, 29; 15, 30; 16, 31; 17, 32; 29, 33; 29, 34; 30, 35; 30, 36; 31, 37; 31, 38; 32, 39; 32, 40; 34, 41; 34, 42; 36, 43; 36, 44... | def list(self, id, filter=None, type=None, sort=None, limit=None, page=None): # pylint: disable=invalid-name,redefined-builtin
"""Get a list of a device's attachments.
:param id: Device ID as an int.
:param filter: (optional) Filters to apply as a string list.
:param type: (optional) `u... |
0, module; 1, function_definition; 2, function_name:_process_value; 3, parameters; 4, block; 5, identifier:self; 6, identifier:value; 7, identifier:type; 8, expression_statement; 9, if_statement; 10, return_statement; 11, comment:"""
Process a value that will be sent to backend
:param value: the value ... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 8, 11; 9, 12; 9, 13; 10, 14; 12, 15; 13, 16; 15, 17; 15, 18; 16, 19; 18, 20; 18, 21; 19, 22; 19, 23; 21, 24; 21, 25; 23, 26; 23, 27; 24, 28; 24, 29; 25, 30; 26, 31; 26, 32; 27, 33 | def _process_value(self, value, type):
"""
Process a value that will be sent to backend
:param value: the value to return
:param type: hint for what sort of value this is
:type type: str
"""
if not isinstance(value, six.string_types + (list,)):
val... |
0, module; 1, function_definition; 2, function_name:representatives; 3, parameters; 4, block; 5, identifier:self; 6, default_parameter; 7, default_parameter; 8, expression_statement; 9, expression_statement; 10, if_statement; 11, if_statement; 12, expression_statement; 13, expression_statement; 14, for_statement; 15, r... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 6, 16; 6, 17; 7, 18; 7, 19; 8, 20; 9, 21; 10, 22; 10, 23; 11, 24; 11, 25; 12, 26; 13, 27; 14, 28; 14, 29; 14, 30; 15, 31; 21, 32; 21, 33; 22, 34; 22, 35; 23, 36; 25, 37; 26, 38; 26, 39; 27, 40; 27, 41; 28, 42; 28, 43; 29, 44... | def representatives(self, count=None, sorting=False):
"""
Returns a list of pairs of representative and its voting weight
:param count: Max amount of representatives to return
:type count: int
:param sorting: If true, sorts by weight
:type sorting: bool
:raises... |
0, module; 1, function_definition; 2, function_name:iterative_overlap_assembly; 3, parameters; 4, block; 5, identifier:variant_sequences; 6, default_parameter; 7, expression_statement; 8, if_statement; 9, comment:# reduce the number of inputs to the merge algorithm by first collapsing; 10, comment:# shorter sequences o... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 6, 17; 6, 18; 7, 19; 8, 20; 8, 21; 8, 22; 8, 23; 11, 24; 12, 25; 13, 26; 14, 27; 15, 28; 16, 29; 20, 30; 20, 31; 23, 32; 24, 33; 24, 34; 25, 35; 25, 36; 26, 37; 26, 38; 27, 39; 27, 40; 28, 41; 28, 42; 29, 43; 29, 44; ... | def iterative_overlap_assembly(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Assembles longer sequences from reads centered on a variant by
between merging all pairs of overlapping sequences and collapsing
shorter sequences onto every longer sequen... |
0, module; 1, function_definition; 2, function_name:rot_consts; 3, parameters; 4, block; 5, identifier:geom; 6, identifier:masses; 7, default_parameter; 8, default_parameter; 9, expression_statement; 10, comment:# Imports; 11, import_statement; 12, import_from_statement; 13, comment:# Ensure units are valid; 14, if_sta... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 4, 18; 4, 19; 4, 20; 4, 21; 4, 22; 4, 23; 4, 24; 4, 25; 4, 26; 7, 27; 7, 28; 8, 29; 8, 30; 9, 31; 11, 32; 12, 33; 12, 34; 12, 35; 12, 36; 12, 37; 14, 38; 14, 39; 18, 40; 20, 41; 20, 42; 20, 43; 20, 44; 23, 45; ... | def rot_consts(geom, masses, units=_EURC.INV_INERTIA, on_tol=_DEF.ORTHONORM_TOL):
"""Rotational constants for a given molecular system.
Calculates the rotational constants for the provided system with numerical
value given in the units provided in `units`. The orthnormality tolerance
`on_tol` is requi... |
0, module; 1, function_definition; 2, function_name:reference_contexts_for_variants; 3, parameters; 4, block; 5, identifier:variants; 6, identifier:context_size; 7, default_parameter; 8, expression_statement; 9, expression_statement; 10, for_statement; 11, return_statement; 12, identifier:transcript_id_whitelist; 13, N... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 4, 11; 7, 12; 7, 13; 8, 14; 9, 15; 10, 16; 10, 17; 10, 18; 11, 19; 15, 20; 15, 21; 18, 22; 21, 23; 21, 24; 22, 25; 25, 26; 25, 27; 26, 28; 26, 29; 27, 30; 27, 31; 31, 32; 31, 33; 31, 34; 32, 35; 32, 36; 33, 37; 33, 38; 34, 39; 34, 40 | def reference_contexts_for_variants(
variants,
context_size,
transcript_id_whitelist=None):
"""
Extract a set of reference contexts for each variant in the collection.
Parameters
----------
variants : varcode.VariantCollection
context_size : int
Max of nucleotid... |
0, module; 1, function_definition; 2, function_name:ffd; 3, parameters; 4, block; 5, identifier:items; 6, identifier:targets; 7, dictionary_splat_pattern; 8, expression_statement; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, return_statement; 13, identifier:kwargs; 14, comment:"""Fir... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 7, 13; 8, 14; 9, 15; 10, 16; 11, 17; 12, 18; 15, 19; 15, 20; 16, 21; 16, 22; 17, 23; 17, 24; 18, 25; 18, 26; 20, 27; 20, 28; 22, 29; 22, 30; 24, 31; 24, 32; 26, 33; 26, 34; 28, 35; 28, 36; 30, 37; 30, 38; 30, 39; 32, 40; 32, 41; 36, 42; 36, 43; ... | def ffd(items, targets, **kwargs):
"""First-Fit Decreasing
This is perhaps the simplest packing heuristic;
it simply packs items in the next available bin.
This algorithm differs only from Next-Fit Decreasing
in having a 'sort'; that is, the items are pre-sorted
(largest to smallest).
Com... |
0, module; 1, function_definition; 2, function_name:sort_protein_sequences; 3, parameters; 4, block; 5, identifier:protein_sequences; 6, expression_statement; 7, return_statement; 8, comment:"""
Sort protein sequences in decreasing order of priority
"""; 9, call; 10, identifier:list; 11, argument_list; 12, call... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 6, 8; 7, 9; 9, 10; 9, 11; 11, 12; 12, 13; 12, 14; 14, 15; 14, 16; 14, 17; 16, 18; 16, 19; 17, 20; 17, 21; 19, 22; 19, 23 | def sort_protein_sequences(protein_sequences):
"""
Sort protein sequences in decreasing order of priority
"""
return list(
sorted(
protein_sequences,
key=ProteinSequence.ascending_sort_key,
reverse=True)) |
0, module; 1, function_definition; 2, function_name:dump; 3, parameters; 4, block; 5, identifier:obj; 6, default_parameter; 7, default_parameter; 8, default_parameter; 9, dictionary_splat_pattern; 10, expression_statement; 11, if_statement; 12, identifier:fp; 13, None; 14, identifier:indent; 15, None; 16, identifier:so... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 4, 10; 4, 11; 6, 12; 6, 13; 7, 14; 7, 15; 8, 16; 8, 17; 9, 18; 10, 19; 11, 20; 11, 21; 11, 22; 21, 23; 21, 24; 22, 25; 23, 26; 24, 27; 24, 28; 24, 29; 25, 30; 26, 31; 26, 32; 29, 33; 30, 34; 32, 35; 32, 36; 33, 37; 34, 38; 34, 39; 35, 40; 35, 41; 36, 42; 37, 43; 37,... | def dump(obj, fp=None, indent=None, sort_keys=False, **kw):
"""
Dump object to a file like object or string.
:param obj:
:param fp: Open file like object
:param int indent: Indent size, default 2
:param bool sort_keys: Optionally sort dictionary keys.
:return: Yaml serialized data.
"""
... |
0, module; 1, function_definition; 2, function_name:sorted_options; 3, parameters; 4, block; 5, identifier:sort_options; 6, expression_statement; 7, return_statement; 8, comment:"""Sort sort options for display.
:param sort_options: A dictionary containing the field name as key and
asc/desc as value.
:... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 6, 8; 7, 9; 9, 10; 9, 11; 10, 12; 10, 13; 11, 14; 11, 15; 12, 16; 12, 17; 13, 18; 13, 19; 14, 20; 14, 21; 15, 22; 15, 23; 16, 24; 17, 25; 17, 26; 18, 27; 19, 28; 23, 29; 23, 30; 26, 31; 28, 32; 28, 33; 28, 34; 29, 35; 29, 36; 30, 37; 30, 38; 32, 39; 32, 40; 33, 41; 33, 42; 35, ... | def sorted_options(sort_options):
"""Sort sort options for display.
:param sort_options: A dictionary containing the field name as key and
asc/desc as value.
:returns: A dictionary with sorting options for Invenio-Search-JS.
"""
return [
{
'title': v['title'],
... |
0, module; 1, function_definition; 2, function_name:info; 3, parameters; 4, block; 5, identifier:self; 6, expression_statement; 7, return_statement; 8, string; 9, call; 10, string_content:Returns information on all the registered checkers.
Sorted by namespace and then name
:returns a list of CheckerInf... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 6, 8; 7, 9; 8, 10; 9, 11; 9, 12; 12, 13; 12, 14; 13, 15; 13, 16; 14, 17; 14, 18; 15, 19; 15, 20; 18, 21; 18, 22; 19, 23; 19, 24; 21, 25; 22, 26; 22, 27; 26, 28; 26, 29; 27, 30; 27, 31 | def info(self):
''' Returns information on all the registered checkers.
Sorted by namespace and then name
:returns a list of CheckerInfo
'''
return sorted(self._checkers.values(), key=lambda x: (x.ns, x.name)) |
0, module; 1, function_definition; 2, function_name:extract_from_text; 3, parameters; 4, block; 5, identifier:text; 6, expression_statement; 7, return_statement; 8, comment:"""
Extract HAL ids from a text.
:param text: The text to extract HAL ids from.
:returns: A list of matching HAL ids.
>>> sorted(... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 6, 8; 7, 9; 9, 10; 9, 11; 10, 12; 10, 13; 11, 14; 14, 15; 14, 16; 14, 17; 15, 18; 15, 19; 16, 20; 16, 21; 17, 22; 21, 23; 21, 24; 22, 25; 22, 26; 23, 27; 23, 28; 24, 29 | def extract_from_text(text):
"""
Extract HAL ids from a text.
:param text: The text to extract HAL ids from.
:returns: A list of matching HAL ids.
>>> sorted(extract_from_text("hal-01258754 hal-01258754v2 foobar"))
['hal-01258754', 'hal-01258754v2']
"""
return tools.remove_duplicates([... |
0, module; 1, function_definition; 2, function_name:_show_documentation; 3, parameters; 4, block; 5, identifier:self; 6, expression_statement; 7, expression_statement; 8, for_statement; 9, expression_statement; 10, expression_statement; 11, if_statement; 12, expression_statement; 13, expression_statement; 14, while_sta... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 6, 15; 7, 16; 8, 17; 8, 18; 8, 19; 9, 20; 10, 21; 11, 22; 11, 23; 12, 24; 13, 25; 14, 26; 14, 27; 16, 28; 16, 29; 17, 30; 17, 31; 18, 32; 18, 33; 19, 34; 20, 35; 20, 36; 21, 37; 21, 38; 22, 39; 22, 40; 23, 41; 24, 42; 24, 43; 25, 4... | def _show_documentation(self):
"""
Shows all documents of the current groundwork app in the console.
Documents are sorted bei its names, except "main", which gets set to the beginning.
"""
documents = []
for key, document in self.app.documents.get().items():
... |
0, module; 1, function_definition; 2, function_name:dispersion_ranking_NN; 3, parameters; 4, block; 5, identifier:self; 6, identifier:nnm; 7, default_parameter; 8, expression_statement; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, expression_statement; 13, expression_statement; 14, e... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 4, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 4, 18; 4, 19; 7, 20; 7, 21; 8, 22; 9, 23; 10, 24; 11, 25; 12, 26; 13, 27; 14, 28; 15, 29; 16, 30; 17, 31; 18, 32; 19, 33; 23, 34; 23, 35; 24, 36; 24, 37; 25, 38; 25, 39; 26, 40; 26, 41; 27, 42; 27, 43; 28, 44; ... | def dispersion_ranking_NN(self, nnm, num_norm_avg=50):
"""Computes the spatial dispersion factors for each gene.
Parameters
----------
nnm - scipy.sparse, float
Square cell-to-cell nearest-neighbor matrix.
num_norm_avg - int, optional, default 50
The top... |
0, module; 1, function_definition; 2, function_name:canonical_ops; 3, parameters; 4, block; 5, identifier:ops; 6, expression_statement; 7, expression_statement; 8, return_statement; 9, string; 10, assignment; 11, identifier:new_ops; 12, string_content:Returns the given operations array sorted with duplicates removed.
... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 4, 8; 6, 9; 7, 10; 8, 11; 9, 12; 10, 13; 10, 14; 14, 15; 14, 16; 16, 17; 16, 18; 17, 19; 17, 20; 18, 21; 18, 22; 20, 23; 22, 24; 22, 25; 24, 26; 25, 27; 25, 28; 27, 29; 27, 30; 28, 31; 28, 32 | def canonical_ops(ops):
''' Returns the given operations array sorted with duplicates removed.
@param ops checker.Ops
@return: checker.Ops
'''
new_ops = sorted(set(ops), key=lambda x: (x.entity, x.action))
return new_ops |
0, module; 1, function_definition; 2, function_name:extract_from_text; 3, parameters; 4, block; 5, identifier:text; 6, expression_statement; 7, comment:# Remove the leading "arxiv:".; 8, return_statement; 9, comment:"""
Extract arXiv IDs from a text.
:param text: The text to extract arXiv IDs from.
:return... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 4, 8; 6, 9; 8, 10; 10, 11; 10, 12; 11, 13; 11, 14; 12, 15; 15, 16; 15, 17; 15, 18; 16, 19; 16, 20; 17, 21; 17, 22; 18, 23; 19, 24; 19, 25; 20, 26; 20, 27; 20, 28; 20, 29; 22, 30; 22, 31; 23, 32; 23, 33; 28, 34; 28, 35; 29, 36; 29, 37; 30, 38; 30, 39; 31, 40; 32, 41; 32, 42; 37,... | def extract_from_text(text):
"""
Extract arXiv IDs from a text.
:param text: The text to extract arXiv IDs from.
:returns: A list of matching arXiv IDs, in canonical form.
>>> sorted(extract_from_text('1506.06690 1506.06690v1 arXiv:1506.06690 arXiv:1506.06690v1 arxiv:1506.06690 arxiv:1506.06690v1 ... |
0, module; 1, function_definition; 2, function_name:serialize_text; 3, parameters; 4, block; 5, identifier:self; 6, expression_statement; 7, if_statement; 8, expression_statement; 9, expression_statement; 10, for_statement; 11, return_statement; 12, string; 13, boolean_operator; 14, block; 15, assignment; 16, assignmen... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 4, 6; 4, 7; 4, 8; 4, 9; 4, 10; 4, 11; 6, 12; 7, 13; 7, 14; 8, 15; 9, 16; 10, 17; 10, 18; 10, 19; 11, 20; 12, 21; 13, 22; 13, 23; 14, 24; 15, 25; 15, 26; 16, 27; 16, 28; 19, 29; 20, 30; 20, 31; 22, 32; 22, 33; 23, 34; 23, 35; 24, 36; 26, 37; 26, 38; 29, 39; 30, 40; 30, 41; 31, 42; 32, 43; 3... | def serialize_text(self):
'''Returns a serialized form of the Namepace.
All the elements in the namespace are sorted by
URI, joined to the associated prefix with a colon and
separated with spaces.
:return: bytes
'''
if self._uri_to_prefix is None or len(self._uri... |
0, module; 1, function_definition; 2, function_name:process; 3, parameters; 4, block; 5, identifier:self; 6, identifier:versions; 7, expression_statement; 8, for_statement; 9, comment:"""Logging version sorted ascending by tool name."""; 10, identifier:tool_name; 11, call; 12, block; 13, identifier:sorted; 14, argument... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 4, 7; 4, 8; 7, 9; 8, 10; 8, 11; 8, 12; 11, 13; 11, 14; 12, 15; 12, 16; 14, 17; 15, 18; 16, 19; 17, 20; 17, 21; 18, 22; 18, 23; 19, 24; 19, 25; 20, 26; 20, 27; 23, 28; 23, 29; 24, 30; 24, 31; 25, 32; 32, 33; 32, 34; 34, 35; 34, 36 | def process(self, versions):
"""Logging version sorted ascending by tool name."""
for tool_name in sorted(versions.keys()):
version = versions[tool_name]
self._log("Using tool '%s', %s" % (tool_name, version)) |
0, module; 1, function_definition; 2, function_name:most_similar_catchments; 3, parameters; 4, block; 5, identifier:self; 6, identifier:subject_catchment; 7, identifier:similarity_dist_function; 8, default_parameter; 9, default_parameter; 10, expression_statement; 11, if_statement; 12, expression_statement; 13, comment... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 4, 16; 4, 17; 4, 18; 4, 19; 4, 20; 4, 21; 4, 22; 4, 23; 4, 24; 4, 25; 8, 26; 8, 27; 9, 28; 9, 29; 10, 30; 11, 31; 11, 32; 12, 33; 14, 34; 16, 35; 16, 36; 16, 37; 18, 38; 18, 39; 18, 40; 20, 41; 22, 42; 23, 43; 24, 44; 24, 45... | def most_similar_catchments(self, subject_catchment, similarity_dist_function, records_limit=500,
include_subject_catchment='auto'):
"""
Return a list of catchments sorted by hydrological similarity defined by `similarity_distance_function`
:param subject_catchme... |
0, module; 1, function_definition; 2, function_name:sort_and_index_star; 3, parameters; 4, block; 5, identifier:job; 6, identifier:star_bams; 7, identifier:univ_options; 8, identifier:star_options; 9, expression_statement; 10, expression_statement; 11, expression_statement; 12, expression_statement; 13, expression_stat... | 0, 1; 1, 2; 1, 3; 1, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, 9; 4, 10; 4, 11; 4, 12; 4, 13; 4, 14; 4, 15; 9, 16; 10, 17; 11, 18; 12, 19; 13, 20; 14, 21; 15, 22; 17, 23; 17, 24; 18, 25; 18, 26; 19, 27; 19, 28; 20, 29; 20, 30; 21, 31; 21, 32; 22, 33; 22, 34; 22, 35; 23, 36; 23, 37; 24, 38; 24, 39; 26, 40; 26, 41; 28, 42; 28, 43; 2... | def sort_and_index_star(job, star_bams, univ_options, star_options):
"""
A wrapper for sorting and indexing the genomic star bam generated by run_star. It is required
since run_star returns a dict of 2 bams
:param dict star_bams: The bams from run_star
:param dict univ_options: Dict of universal op... |
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