text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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def parse(db_folder, out_folder):
""" Parse a cronos database. Convert the database located in ``db_folder`` into CSV files in the directory ``out_folder``. """ |
# The database structure, containing table and column definitions as
# well as other data.
stru_dat = get_file(db_folder, 'CroStru.dat')
# Index file for the database, which contains offsets for each record.
data_tad = get_file(db_folder, 'CroBank.tad')
# Actual data records, can only be decode... |
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def encode1(self):
"""Return the base64 encoding of the figure file and insert in html image tag.""" |
data_uri = b64encode(open(self.path, 'rb').read()).decode('utf-8').replace('\n', '')
return '<img src="data:image/png;base64,{0}">'.format(data_uri) |
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def encode2(self):
"""Return the base64 encoding of the fig attribute and insert in html image tag.""" |
buf = BytesIO()
self.fig.savefig(buf, format='png', bbox_inches='tight', dpi=100)
buf.seek(0)
string = b64encode(buf.read())
return '<img src="data:image/png;base64,{0}">'.format(urlquote(string)) |
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def loadFromDisk(self, calculation):
""" Read the spectra from the files generated by Quanty and store them as a list of spectum objects. """ |
suffixes = {
'Isotropic': 'iso',
'Circular Dichroism (R-L)': 'cd',
'Right Polarized (R)': 'r',
'Left Polarized (L)': 'l',
'Linear Dichroism (V-H)': 'ld',
'Vertical Polarized (V)': 'v',
'Horizontal Polarized (H)': 'h',
... |
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def updateResultsView(self, index):
""" Update the selection to contain only the result specified by the index. This should be the last index of the model. Final... |
flags = (QItemSelectionModel.Clear | QItemSelectionModel.Rows |
QItemSelectionModel.Select)
self.resultsView.selectionModel().select(index, flags)
self.resultsView.resizeColumnsToContents()
self.resultsView.setFocus() |
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def updatePlotWidget(self):
"""Updating the plotting widget should not require any information about the current state of the widget.""" |
pw = self.getPlotWidget()
pw.reset()
results = self.resultsModel.getCheckedItems()
for result in results:
if isinstance(result, ExperimentalData):
spectrum = result.spectra['Expt']
spectrum.legend = '{}-{}'.format(result.index, 'Expt')
... |
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def row(self):
"""Return the row of the child.""" |
if self.parent is not None:
children = self.parent.getChildren()
# The index method of the list object.
return children.index(self)
else:
return 0 |
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def parent(self, index):
"""Return the index of the parent for a given index of the child. Unfortunately, the name of the method has to be parent, even though a ... |
childItem = self.item(index)
parentItem = childItem.parent
if parentItem == self.rootItem:
parentIndex = QModelIndex()
else:
parentIndex = self.createIndex(parentItem.row(), 0, parentItem)
return parentIndex |
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def setData(self, index, value, role):
"""Set the role data for the item at index to value.""" |
if not index.isValid():
return False
item = self.item(index)
column = index.column()
if role == Qt.EditRole:
items = list()
items.append(item)
if self.sync:
parentIndex = self.parent(index)
# Iterate over... |
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def flags(self, index):
"""Return the active flags for the given index. Add editable flag to items other than the first column. """ |
activeFlags = (Qt.ItemIsEnabled | Qt.ItemIsSelectable |
Qt.ItemIsUserCheckable)
item = self.item(index)
column = index.column()
if column > 0 and not item.childCount():
activeFlags = activeFlags | Qt.ItemIsEditable
return activeFlags |
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def _getModelData(self, modelData, parentItem=None):
"""Return the data contained in the model.""" |
if parentItem is None:
parentItem = self.rootItem
for item in parentItem.getChildren():
key = item.getItemData(0)
if item.childCount():
modelData[key] = odict()
self._getModelData(modelData[key], item)
else:
... |
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def _contextMenu(self, pos):
"""Handle plot area customContextMenuRequested signal. :param QPoint pos: Mouse position relative to plot area """ |
# Create the context menu.
menu = QMenu(self)
menu.addAction(self._zoomBackAction)
# Displaying the context menu at the mouse position requires
# a global position.
# The position received as argument is relative to PlotWidget's
# plot area, and thus needs to be... |
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def convolve_fft(array, kernel):
""" Convolve an array with a kernel using FFT. Implemntation based on the convolve_fft function from astropy. https://github.com... |
array = np.asarray(array, dtype=np.complex)
kernel = np.asarray(kernel, dtype=np.complex)
if array.ndim != kernel.ndim:
raise ValueError("Image and kernel must have same number of "
"dimensions")
array_shape = array.shape
kernel_shape = kernel.shape
new_shape... |
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| def diagonalize(self):
'''Diagonalize the tensor.'''
self.eigvals, self.eigvecs = np.linalg.eig(
(self.tensor.transpose() + self.tensor) / 2.0)
self.eigvals = np.diag(np.dot(
np.dot(self.eigvecs.transpose(), self.tensor), self.eigvecs)) |
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| def _skip_lines(self, n):
'''Skip a number of lines from the output.'''
for i in range(n):
self.line = next(self.output)
return self.line |
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| def _parse_tensor(self, indices=False):
'''Parse a tensor.'''
if indices:
self.line = self._skip_lines(1)
tensor = np.zeros((3, 3))
for i in range(3):
tokens = self.line.split()
if indices:
tensor[i][0] = float(tokens[1])
... |
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def __validate(self, target, value, oldvalue, initiator):
""" Method executed when the event 'set' is triggered. :param target: Object triggered :param value: Ne... |
if value == oldvalue:
return value
if self.allow_null and value is None:
return value
if self.check_value(value):
return value
else:
if self.throw_exception:
if self.message:
self.message = self.messag... |
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def __create_event(self):
""" Create an SQLAlchemy event listening the 'set' in a particular column. :rtype : object """ |
if not event.contains(self.field, 'set', self.__validate):
event.listen(self.field, 'set', self.__validate, retval=True) |
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def stop(self):
""" Remove the listener to stop the validation """ |
if event.contains(self.field, 'set', self.__validate):
event.remove(self.field, 'set', self.__validate) |
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def start(self):
""" Restart the listener """ |
if not event.contains(self.field, 'set', self.__validate):
self.__create_event() |
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def nhapDaiHan(self, cucSo, gioiTinh):
"""Nhap dai han Args: cucSo (TYPE):
Description gioiTinh (TYPE):
Description Returns: TYPE: Description """ |
for cung in self.thapNhiCung:
khoangCach = khoangCachCung(cung.cungSo, self.cungMenh, gioiTinh)
cung.daiHan(cucSo + khoangCach * 10)
return self |
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def nt2aa(ntseq):
"""Translate a nucleotide sequence into an amino acid sequence. Parameters ntseq : str Nucleotide sequence composed of A, C, G, or T (uppercase... |
nt2num = {'A': 0, 'C': 1, 'G': 2, 'T': 3, 'a': 0, 'c': 1, 'g': 2, 't': 3}
aa_dict ='KQE*TPASRRG*ILVLNHDYTPASSRGCILVFKQE*TPASRRGWMLVLNHDYTPASSRGCILVF'
return ''.join([aa_dict[nt2num[ntseq[i]] + 4*nt2num[ntseq[i+1]] + 16*nt2num[ntseq[i+2]]] for i in range(0, len(ntseq), 3) if i+2 < len(ntseq)]) |
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def nt2codon_rep(ntseq):
"""Represent nucleotide sequence by sequence of codon symbols. 'Translates' the nucleotide sequence into a symbolic representation of 'a... |
#
nt2num = {'A': 0, 'C': 1, 'G': 2, 'T': 3, 'a': 0, 'c': 1, 'g': 2, 't': 3}
#Use single characters not in use to represent each individual codon --- this function is called in constructing the codon dictionary
codon_rep ='\x80\x81\x82\x83\x84\x85\x86\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92... |
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def cutR_seq(seq, cutR, max_palindrome):
"""Cut genomic sequence from the right. Parameters seq : str Nucleotide sequence to be cut from the right cutR : int cut... |
complement_dict = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'} #can include lower case if wanted
if cutR < max_palindrome:
seq = seq + ''.join([complement_dict[nt] for nt in seq[cutR - max_palindrome:]][::-1]) #reverse complement palindrome insertions
else:
seq = seq[:len(seq) - cutR + max_pali... |
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def cutL_seq(seq, cutL, max_palindrome):
"""Cut genomic sequence from the left. Parameters seq : str Nucleotide sequence to be cut from the right cutL : int cutL... |
complement_dict = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'} #can include lower case if wanted
if cutL < max_palindrome:
seq = ''.join([complement_dict[nt] for nt in seq[:max_palindrome - cutL]][::-1]) + seq #reverse complement palindrome insertions
else:
seq = seq[cutL-max_palindrome:] ... |
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def generate_sub_codons_left(codons_dict):
"""Generate the sub_codons_left dictionary of codon prefixes. Parameters codons_dict : dict Dictionary, keyed by the a... |
sub_codons_left = {}
for aa in codons_dict.keys():
sub_codons_left[aa] = list(set([x[0] for x in codons_dict[aa]] + [x[:2] for x in codons_dict[aa]]))
return sub_codons_left |
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def calc_steady_state_dist(R):
"""Calculate the steady state dist of a 4 state markov transition matrix. Parameters R : ndarray Markov transition matrix Returns ... |
#Calc steady state distribution for a dinucleotide bias matrix
w, v = np.linalg.eig(R)
for i in range(4):
if np.abs(w[i] - 1) < 1e-8:
return np.real(v[:, i] / np.sum(v[:, i]))
return -1 |
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def rnd_ins_seq(ins_len, C_R, CP_first_nt):
"""Generate a random insertion nucleotide sequence of length ins_len. Draws the sequence identity (for a set length) ... |
nt2num = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
num2nt = 'ACGT'
if ins_len == 0:
return ''
seq = num2nt[CP_first_nt.searchsorted(np.random.random())]
ins_len += -1
while ins_len > 0:
seq += num2nt[C_R[nt2num[seq[-1]], :].searchsorted(np.random.random())]
ins_len += -1
... |
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def update_rates(self):
""" Creates or updates rates for a source """ |
source, created = RateSource.objects.get_or_create(name=self.get_source_name())
source.base_currency = self.get_base_currency()
source.save()
for currency, value in six.iteritems(self.get_rates()):
try:
rate = Rate.objects.get(source=source, currency=currenc... |
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def showDosHeaderData(peInstance):
""" Prints IMAGE_DOS_HEADER fields. """ |
dosFields = peInstance.dosHeader.getFields()
print "[+] IMAGE_DOS_HEADER values:\n"
for field in dosFields:
if isinstance(dosFields[field], datatypes.Array):
print "--> %s - Array of length %d" % (field, len(dosFields[field]))
counter = 0
for element in do... |
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def showFileHeaderData(peInstance):
""" Prints IMAGE_FILE_HEADER fields. """ |
fileHeaderFields = peInstance.ntHeaders.fileHeader.getFields()
print "[+] IMAGE_FILE_HEADER values:\n"
for field in fileHeaderFields:
print "--> %s = 0x%08x" % (field, fileHeaderFields[field].value) |
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def showOptionalHeaderData(peInstance):
""" Prints IMAGE_OPTIONAL_HEADER fields. """ |
print "[+] IMAGE_OPTIONAL_HEADER:\n"
ohFields = peInstance.ntHeaders.optionalHeader.getFields()
for field in ohFields:
if not isinstance(ohFields[field], datadirs.DataDirectory):
print "--> %s = 0x%08x" % (field, ohFields[field].value) |
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def showDataDirectoriesData(peInstance):
""" Prints the DATA_DIRECTORY fields. """ |
print "[+] Data directories:\n"
dirs = peInstance.ntHeaders.optionalHeader.dataDirectory
counter = 1
for dir in dirs:
print "[%d] --> Name: %s -- RVA: 0x%08x -- SIZE: 0x%08x" % (counter, dir.name.value, dir.rva.value, dir.size.value)
counter += 1 |
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def showSectionsHeaders(peInstance):
""" Prints IMAGE_SECTION_HEADER for every section present in the file. """ |
print "[+] Sections information:\n"
print "--> NumberOfSections: %d\n" % peInstance.ntHeaders.fileHeader.numberOfSections.value
for section in peInstance.sectionHeaders:
fields = section.getFields()
for field in fields:
if isinstance(fields[field], datatypes.String):
... |
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def showImports(peInstance):
""" Shows imports information. """ |
iidEntries = peInstance.ntHeaders.optionalHeader.dataDirectory[consts.IMPORT_DIRECTORY].info
if iidEntries:
for iidEntry in iidEntries:
fields = iidEntry.getFields()
print "module: %s" % iidEntry.metaData.moduleName.value
for field in fields:
pri... |
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def showExports(peInstance):
""" Show exports information """ |
exports = peInstance.ntHeaders.optionalHeader.dataDirectory[consts.EXPORT_DIRECTORY].info
if exports:
exp_fields = exports.getFields()
for field in exp_fields:
print "%s -> %x" % (field, exp_fields[field].value)
for entry in exports.exportTable:
entry_... |
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def getFields(self):
""" Returns all the class attributues. @rtype: dict @return: A dictionary containing all the class attributes. """ |
d = {}
for i in self._attrsList:
key = i
value = getattr(self, i)
d[key] = value
return d |
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| def calc_euler_tour(g, start, end):
'''Calculates an Euler tour over the graph g from vertex start to vertex end.
Assumes start and end are odd-degree vertices and that there are no other odd-degree
vertices.'''
even_g = nx.subgraph(g, g.nodes()).copy()
if end in even_g.neighbors(start):
# I... |
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| def greedy_trails(subg, odds, verbose):
'''Greedily select trails by making the longest you can until the end'''
if verbose:
print('\tCreating edge map')
edges = defaultdict(list)
for x,y in subg.edges():
edges[x].append(y)
edges[y].append(x)
if verbose:
print('\tS... |
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| def decompose_graph(g, heuristic='tour', max_odds=20, verbose=0):
'''Decompose a graph into a set of non-overlapping trails.'''
# Get the connected subgraphs
subgraphs = [nx.subgraph(g, x).copy() for x in nx.connected_components(g)]
chains = []
num_subgraphs = len(subgraphs)
step = 0
while ... |
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def lerp(self, a, t):
""" Lerp. Linear interpolation from self to a""" |
return self.plus(a.minus(self).times(t)); |
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def interpolate(self, other, t):
""" Create a new vertex between this vertex and `other` by linearly interpolating all properties using a parameter of `t`. Subcl... |
return Vertex(self.pos.lerp(other.pos, t),
self.normal.lerp(other.normal, t)) |
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def splitPolygon(self, polygon, coplanarFront, coplanarBack, front, back):
""" Split `polygon` by this plane if needed, then put the polygon or polygon fragments... |
COPLANAR = 0 # all the vertices are within EPSILON distance from plane
FRONT = 1 # all the vertices are in front of the plane
BACK = 2 # all the vertices are at the back of the plane
SPANNING = 3 # some vertices are in front, some in the back
# Classify each point as well as th... |
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def invert(self):
""" Convert solid space to empty space and empty space to solid space. """ |
for poly in self.polygons:
poly.flip()
self.plane.flip()
if self.front:
self.front.invert()
if self.back:
self.back.invert()
temp = self.front
self.front = self.back
self.back = temp |
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def clipPolygons(self, polygons):
""" Recursively remove all polygons in `polygons` that are inside this BSP tree. """ |
if not self.plane:
return polygons[:]
front = []
back = []
for poly in polygons:
self.plane.splitPolygon(poly, front, back, front, back)
if self.front:
front = self.front.clipPolygons(front)
if self.back:
back = self.... |
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def clipTo(self, bsp):
""" Remove all polygons in this BSP tree that are inside the other BSP tree `bsp`. """ |
self.polygons = bsp.clipPolygons(self.polygons)
if self.front:
self.front.clipTo(bsp)
if self.back:
self.back.clipTo(bsp) |
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def allPolygons(self):
""" Return a list of all polygons in this BSP tree. """ |
polygons = self.polygons[:]
if self.front:
polygons.extend(self.front.allPolygons())
if self.back:
polygons.extend(self.back.allPolygons())
return polygons |
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def get_rate(currency):
"""Returns the rate from the default currency to `currency`.""" |
source = get_rate_source()
try:
return Rate.objects.get(source=source, currency=currency).value
except Rate.DoesNotExist:
raise CurrencyConversionException(
"Rate for %s in %s do not exists. "
"Please run python manage.py update_rates" % (
currency, s... |
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def get_rate_source():
"""Get the default Rate Source and return it.""" |
backend = money_rates_settings.DEFAULT_BACKEND()
try:
return RateSource.objects.get(name=backend.get_source_name())
except RateSource.DoesNotExist:
raise CurrencyConversionException(
"Rate for %s source do not exists. "
"Please run python manage.py update_rates" % ba... |
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def base_convert_money(amount, currency_from, currency_to):
""" Convert 'amount' from 'currency_from' to 'currency_to' """ |
source = get_rate_source()
# Get rate for currency_from.
if source.base_currency != currency_from:
rate_from = get_rate(currency_from)
else:
# If currency from is the same as base currency its rate is 1.
rate_from = Decimal(1)
# Get rate for currency_to.
rate_to = get_... |
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def convert_money(amount, currency_from, currency_to):
""" Convert 'amount' from 'currency_from' to 'currency_to' and return a Money instance of the converted am... |
new_amount = base_convert_money(amount, currency_from, currency_to)
return moneyed.Money(new_amount, currency_to) |
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def format_date(format_string=None, datetime_obj=None):
""" Format a datetime object with Java SimpleDateFormat's-like string. If datetime_obj is not given - use... |
datetime_obj = datetime_obj or datetime.now()
if format_string is None:
seconds = int(datetime_obj.strftime("%s"))
milliseconds = datetime_obj.microsecond // 1000
return str(seconds * 1000 + milliseconds)
else:
formatter = SimpleDateFormat(format_string)
return forma... |
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def allZero(buffer):
""" Tries to determine if a buffer is empty. @type buffer: str @param buffer: Buffer to test if it is empty. @rtype: bool @return: C{True} i... |
allZero = True
for byte in buffer:
if byte != "\x00":
allZero = False
break
return allZero |
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def readAlignedString(self, align = 4):
""" Reads an ASCII string aligned to the next align-bytes boundary. @type align: int @param align: (Optional) The value w... |
s = self.readString()
r = align - len(s) % align
while r:
s += self.data[self.offset]
self.offset += 1
r -= 1
return s.rstrip("\x00") |
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def readAt(self, offset, size):
""" Reads as many bytes indicated in the size parameter at the specific offset. @type offset: int @param offset: Offset of the va... |
if offset > self.length:
if self.log:
print "Warning: Trying to read: %d bytes - only %d bytes left" % (nroBytes, self.length - self.offset)
offset = self.length - self.offset
tmpOff = self.tell()
self.setOffset(offset)
r = self.read(size)
... |
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def send(self, message, channel_name=None, fail_silently=False, options=None):
# type: (Text, Optional[str], bool, Optional[SendOptions]) -> None """Send a notif... |
if channel_name is None:
channels = self.settings["CHANNELS"]
else:
try:
channels = {
"__selected__": self.settings["CHANNELS"][channel_name]
}
except KeyError:
raise Exception("channels does not exi... |
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def request(self, method, path, params=None, headers=None, cookies=None, data=None, json=None, allow_redirects=None, timeout=None):
""" Prepares and sends an HTT... |
headers = headers or {}
timeout = timeout if timeout is not None else self._timeout
allow_redirects = allow_redirects if allow_redirects is not None else self._allow_redirects
if self._keep_alive and self.__session is None:
self.__session = requests.Session()
if se... |
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def load_genomic_CDR3_anchor_pos_and_functionality(anchor_pos_file_name):
"""Read anchor position and functionality from file. Parameters anchor_pos_file_name : ... |
anchor_pos_and_functionality = {}
anchor_pos_file = open(anchor_pos_file_name, 'r')
first_line = True
for line in anchor_pos_file:
if first_line:
first_line = False
continue
split_line = line.split(',')
split_line = [x.strip() for x in ... |
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def generate_cutV_genomic_CDR3_segs(self):
"""Add palindromic inserted nucleotides to germline V sequences. The maximum number of palindromic insertions are appe... |
max_palindrome = self.max_delV_palindrome
self.cutV_genomic_CDR3_segs = []
for CDR3_V_seg in [x[1] for x in self.genV]:
if len(CDR3_V_seg) < max_palindrome:
self.cutV_genomic_CDR3_segs += [cutR_seq(CDR3_V_seg, 0, len(CDR3_V_seg))]
else:
... |
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def generate_cutJ_genomic_CDR3_segs(self):
"""Add palindromic inserted nucleotides to germline J sequences. The maximum number of palindromic insertions are appe... |
max_palindrome = self.max_delJ_palindrome
self.cutJ_genomic_CDR3_segs = []
for CDR3_J_seg in [x[1] for x in self.genJ]:
if len(CDR3_J_seg) < max_palindrome:
self.cutJ_genomic_CDR3_segs += [cutL_seq(CDR3_J_seg, 0, len(CDR3_J_seg))]
else:
... |
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def generate_cutD_genomic_CDR3_segs(self):
"""Add palindromic inserted nucleotides to germline V sequences. The maximum number of palindromic insertions are appe... |
max_palindrome_L = self.max_delDl_palindrome
max_palindrome_R = self.max_delDr_palindrome
self.cutD_genomic_CDR3_segs = []
for CDR3_D_seg in [x[1] for x in self.genD]:
if len(CDR3_D_seg) < min(max_palindrome_L, max_palindrome_R):
self.cutD_genomic_CDR3_segs ... |
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| def verify_and_fill_address_paths_from_bip32key(address_paths, master_key, network):
'''
Take address paths and verifies their accuracy client-side.
Also fills in all the available metadata (WIF, public key, etc)
'''
assert network, network
wallet_obj = Wallet.deserialize(master_key, network=... |
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| def run(self, lam, initial_values=None):
'''Run the graph-fused logit lasso with a fixed lambda penalty.'''
if initial_values is not None:
if self.k == 0 and self.trails is not None:
betas, zs, us = initial_values
else:
betas, us = initial_values
... |
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| def data_log_likelihood(self, successes, trials, beta):
'''Calculates the log-likelihood of a Polya tree bin given the beta values.'''
return binom.logpmf(successes, trials, 1.0 / (1 + np.exp(-beta))).sum() |
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def spawn_worker(params):
""" This method has to be module level function :type params: Params """ |
setup_logging(params)
log.info("Adding worker: idx=%s\tconcurrency=%s\tresults=%s", params.worker_index, params.concurrency,
params.report)
worker = Worker(params)
worker.start()
worker.join() |
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| def create_plateaus(data, edges, plateau_size, plateau_vals, plateaus=None):
'''Creates plateaus of constant value in the data.'''
nodes = set(edges.keys())
if plateaus is None:
plateaus = []
for i in range(len(plateau_vals)):
if len(nodes) == 0:
break
... |
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| def pretty_str(p, decimal_places=2, print_zero=True, label_columns=False):
'''Pretty-print a matrix or vector.'''
if len(p.shape) == 1:
return vector_str(p, decimal_places, print_zero)
if len(p.shape) == 2:
return matrix_str(p, decimal_places, print_zero, label_columns)
raise Exception('... |
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| def matrix_str(p, decimal_places=2, print_zero=True, label_columns=False):
'''Pretty-print the matrix.'''
return '[{0}]'.format("\n ".join([(str(i) if label_columns else '') + vector_str(a, decimal_places, print_zero) for i, a in enumerate(p)])) |
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| def vector_str(p, decimal_places=2, print_zero=True):
'''Pretty-print the vector values.'''
style = '{0:.' + str(decimal_places) + 'f}'
return '[{0}]'.format(", ".join([' ' if not print_zero and a == 0 else style.format(a) for a in p])) |
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| def nearly_unique(arr, rel_tol=1e-4, verbose=0):
'''Heuristic method to return the uniques within some precision in a numpy array'''
results = np.array([arr[0]])
for x in arr:
if np.abs(results - x).min() > rel_tol:
results = np.append(results, x)
return results |
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| def get_delta(D, k):
'''Calculate the k-th order trend filtering matrix given the oriented edge
incidence matrix and the value of k.'''
if k < 0:
raise Exception('k must be at least 0th order.')
result = D
for i in range(k):
result = D.T.dot(result) if i % 2 == 0 else D.dot(result)
... |
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| def decompose_delta(deltak):
'''Decomposes the k-th order trend filtering matrix into a c-compatible set
of arrays.'''
if not isspmatrix_coo(deltak):
deltak = coo_matrix(deltak)
dk_rows = deltak.shape[0]
dk_rowbreaks = np.cumsum(deltak.getnnz(1), dtype="int32")
dk_cols = deltak.col.astyp... |
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def hasMZSignature(self, rd):
""" Check for MZ signature. @type rd: L{ReadData} @param rd: A L{ReadData} object. @rtype: bool @return: True is the given L{ReadDa... |
rd.setOffset(0)
sign = rd.read(2)
if sign == "MZ":
return True
return False |
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def hasPESignature(self, rd):
""" Check for PE signature. @type rd: L{ReadData} @param rd: A L{ReadData} object. @rtype: bool @return: True is the given L{ReadDa... |
rd.setOffset(0)
e_lfanew_offset = unpack("<L", rd.readAt(0x3c, 4))[0]
sign = rd.readAt(e_lfanew_offset, 2)
if sign == "PE":
return True
return False |
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def validate(self):
""" Performs validations over some fields of the PE structure to determine if the loaded file has a valid PE format. @raise PEException: If a... |
# Ange Albertini (@angie4771) can kill me for this! :)
if self.dosHeader.e_magic.value != consts.MZ_SIGNATURE:
raise excep.PEException("Invalid MZ signature. Found %d instead of %d." % (self.dosHeader.magic.value, consts.MZ_SIGNATURE))
if self.dosHeader.e_lfanew.value > len... |
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def readFile(self, pathToFile):
""" Returns data from a file. @type pathToFile: str @param pathToFile: Path to the file. @rtype: str @return: The data from file.... |
fd = open(pathToFile, "rb")
data = fd.read()
fd.close()
return data |
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def _getPaddingDataToSectionOffset(self):
""" Returns the data between the last section header and the begenning of data from the first section. @rtype: str @ret... |
start = self._getPaddingToSectionOffset()
end = self.sectionHeaders[0].pointerToRawData.value - start
return self._data[start:start+end] |
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def _getSignature(self, readDataInstance, dataDirectoryInstance):
""" Returns the digital signature within a digital signed PE file. @type readDataInstance: L{Re... |
signature = ""
if readDataInstance is not None and dataDirectoryInstance is not None:
securityDirectory = dataDirectoryInstance[consts.SECURITY_DIRECTORY]
if(securityDirectory.rva.value and securityDirectory.size.value):
readDataInstance.set... |
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def _getOverlay(self, readDataInstance, sectionHdrsInstance):
""" Returns the overlay data from the PE file. @type readDataInstance: L{ReadData} @param readDataI... |
if readDataInstance is not None and sectionHdrsInstance is not None:
# adjust the offset in readDataInstance to the RawOffset + RawSize of the last section
try:
offset = sectionHdrsInstance[-1].pointerToRawData.value + sectionHdrsInstance[-1].sizeOfRawData.va... |
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def getOffsetFromRva(self, rva):
""" Converts an offset to an RVA. @type rva: int @param rva: The RVA to be converted. @rtype: int @return: An integer value repr... |
offset = -1
s = self.getSectionByRva(rva)
if s != offset:
offset = (rva - self.sectionHeaders[s].virtualAddress.value) + self.sectionHeaders[s].pointerToRawData.value
else:
offset = rva
return offset |
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def getRvaFromOffset(self, offset):
""" Converts a RVA to an offset. @type offset: int @param offset: The offset value to be converted to RVA. @rtype: int @retur... |
rva = -1
s = self.getSectionByOffset(offset)
if s:
rva = (offset - self.sectionHeaders[s].pointerToRawData.value) + self.sectionHeaders[s].virtualAddress.value
return rva |
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def getSectionByOffset(self, offset):
""" Given an offset in the file, tries to determine the section this offset belong to. @type offset: int @param offset: Off... |
index = -1
for i in range(len(self.sectionHeaders)):
if (offset < self.sectionHeaders[i].pointerToRawData.value + self.sectionHeaders[i].sizeOfRawData.value):
index = i
break
return index |
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def getSectionIndexByName(self, name):
""" Given a string representing a section name, tries to find the section index. @type name: str @param name: A section na... |
index = -1
if name:
for i in range(len(self.sectionHeaders)):
if self.sectionHeaders[i].name.value.find(name) >= 0:
index = i
break
return index |
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def getSectionByRva(self, rva):
""" Given a RVA in the file, tries to determine the section this RVA belongs to. @type rva: int @param rva: RVA value. @rtype: in... |
index = -1
if rva < self.sectionHeaders[0].virtualAddress.value:
return index
for i in range(len(self.sectionHeaders)):
fa = self.ntHeaders.optionalHeader.fileAlignment.value
prd = self.sectionHeaders[i].pointerToRawData.value
sr... |
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def _getPaddingToSectionOffset(self):
""" Returns the offset to last section header present in the PE file. @rtype: int @return: The offset where the end of the ... |
return len(str(self.dosHeader) + str(self.dosStub) + str(self.ntHeaders) + str(self.sectionHeaders)) |
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def fullLoad(self):
"""Parse all the directories in the PE file.""" |
self._parseDirectories(self.ntHeaders.optionalHeader.dataDirectory, self.PE_TYPE) |
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def _fixPe(self):
""" Fixes the necessary fields in the PE file instance in order to create a valid PE32. i.e. SizeOfImage. """ |
sizeOfImage = 0
for sh in self.sectionHeaders:
sizeOfImage += sh.misc
self.ntHeaders.optionaHeader.sizeoOfImage.value = self._sectionAlignment(sizeOfImage + 0x1000) |
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def getDataAtRva(self, rva, size):
""" Gets binary data at a given RVA. @type rva: int @param rva: The RVA to get the data from. @type size: int @param size: The... |
return self.getDataAtOffset(self.getOffsetFromRva(rva), size) |
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def getDataAtOffset(self, offset, size):
""" Gets binary data at a given offset. @type offset: int @param offset: The offset to get the data from. @type size: in... |
data = str(self)
return data[offset:offset+size] |
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def _parseDelayImportDirectory(self, rva, size, magic = consts.PE32):
""" Parses the delay imports directory. @type rva: int @param rva: The RVA where the delay ... |
return self.getDataAtRva(rva, size) |
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def _parseBoundImportDirectory(self, rva, size, magic = consts.PE32):
""" Parses the bound import directory. @type rva: int @param rva: The RVA where the bound i... |
data = self.getDataAtRva(rva, size)
rd = utils.ReadData(data)
boundImportDirectory = directories.ImageBoundImportDescriptor.parse(rd)
# parse the name of every bounded import.
for i in range(len(boundImportDirectory) - 1):
if hasattr(boundImportDirectory[i],... |
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def _parseLoadConfigDirectory(self, rva, size, magic = consts.PE32):
""" Parses IMAGE_LOAD_CONFIG_DIRECTORY. @type rva: int @param rva: The RVA where the IMAGE_L... |
# print "RVA: %x - SIZE: %x" % (rva, size)
# I've found some issues when parsing the IMAGE_LOAD_CONFIG_DIRECTORY in some DLLs.
# There is an inconsistency with the size of the struct between MSDN docs and VS.
# sizeof(IMAGE_LOAD_CONFIG_DIRECTORY) should be 0x40, in fact, that's the si... |
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def _parseTlsDirectory(self, rva, size, magic = consts.PE32):
""" Parses the TLS directory. @type rva: int @param rva: The RVA where the TLS directory starts. @t... |
data = self.getDataAtRva(rva, size)
rd = utils.ReadData(data)
if magic == consts.PE32:
return directories.TLSDirectory.parse(rd)
elif magic == consts.PE64:
return directories.TLSDirectory64.parse(rd)
else:
raise excep.InvalidParameter... |
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def _parseRelocsDirectory(self, rva, size, magic = consts.PE32):
""" Parses the relocation directory. @type rva: int @param rva: The RVA where the relocation dir... |
data = self.getDataAtRva(rva, size)
#print "Length Relocation data: %x" % len(data)
rd = utils.ReadData(data)
relocsArray = directories.ImageBaseRelocation()
while rd.offset < size:
relocEntry = directories.ImageBaseRelocationEntry.parse(rd)
rel... |
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| def get_addresses_on_both_chains(wallet_obj, used=None, zero_balance=None):
'''
Get addresses across both subchains based on the filter criteria passed in
Returns a list of dicts of the following form:
[
{'address': '1abc123...', 'path': 'm/0/9', 'pubkeyhex': '0123456...'},
... |
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| def dump_all_keys_or_addrs(wallet_obj):
'''
Offline-enabled mechanism to dump addresses
'''
print_traversal_warning()
puts('\nDo you understand this warning?')
if not confirm(user_prompt=DEFAULT_PROMPT, default=False):
puts(colored.red('Dump Cancelled!'))
return
mpub = wal... |
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| def dump_selected_keys_or_addrs(wallet_obj, used=None, zero_balance=None):
'''
Works for both public key only or private key access
'''
if wallet_obj.private_key:
content_str = 'private keys'
else:
content_str = 'addresses'
if not USER_ONLINE:
puts(colored.red('\nInterne... |
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| def dump_private_keys_or_addrs_chooser(wallet_obj):
'''
Offline-enabled mechanism to dump everything
'''
if wallet_obj.private_key:
puts('Which private keys and addresses do you want?')
else:
puts('Which addresses do you want?')
with indent(2):
puts(colored.cyan('1: Acti... |
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def _send_merge_commands(self, config, file_config):
""" Netmiko is being used to push set commands. """ |
if self.loaded is False:
if self._save_backup() is False:
raise MergeConfigException('Error while storing backup '
'config.')
if self.ssh_connection is False:
self._open_ssh()
if file_config:
if isin... |
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def compare_config(self):
""" Netmiko is being used to obtain config diffs because pan-python doesn't support the needed command. """ |
if self.ssh_connection is False:
self._open_ssh()
self.ssh_device.exit_config_mode()
diff = self.ssh_device.send_command("show config diff")
return diff.strip() |
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