repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
CellProfiler/centrosome | centrosome/haralick.py | normalized_per_object | def normalized_per_object(image, labels):
"""Normalize the intensities of each object to the [0, 1] range."""
nobjects = labels.max()
objects = np.arange(nobjects + 1)
lmin, lmax = scind.extrema(image, labels, objects)[:2]
# Divisor is the object's max - min, or 1 if they are the same.
divisor =... | python | def normalized_per_object(image, labels):
"""Normalize the intensities of each object to the [0, 1] range."""
nobjects = labels.max()
objects = np.arange(nobjects + 1)
lmin, lmax = scind.extrema(image, labels, objects)[:2]
# Divisor is the object's max - min, or 1 if they are the same.
divisor =... | Normalize the intensities of each object to the [0, 1] range. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L16-L24 |
CellProfiler/centrosome | centrosome/haralick.py | quantize | def quantize(image, nlevels):
"""Quantize an image into integers 0, 1, ..., nlevels - 1.
image -- a numpy array of type float, range [0, 1]
nlevels -- an integer
"""
tmp = np.array(image // (1.0 / nlevels), dtype='i1')
return tmp.clip(0, nlevels - 1) | python | def quantize(image, nlevels):
"""Quantize an image into integers 0, 1, ..., nlevels - 1.
image -- a numpy array of type float, range [0, 1]
nlevels -- an integer
"""
tmp = np.array(image // (1.0 / nlevels), dtype='i1')
return tmp.clip(0, nlevels - 1) | Quantize an image into integers 0, 1, ..., nlevels - 1.
image -- a numpy array of type float, range [0, 1]
nlevels -- an integer | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L26-L33 |
CellProfiler/centrosome | centrosome/haralick.py | cooccurrence | def cooccurrence(quantized_image, labels, scale_i=3, scale_j=0):
"""Calculates co-occurrence matrices for all the objects in the image.
Return an array P of shape (nobjects, nlevels, nlevels) such that
P[o, :, :] is the cooccurence matrix for object o.
quantized_image -- a numpy array of integer type
... | python | def cooccurrence(quantized_image, labels, scale_i=3, scale_j=0):
"""Calculates co-occurrence matrices for all the objects in the image.
Return an array P of shape (nobjects, nlevels, nlevels) such that
P[o, :, :] is the cooccurence matrix for object o.
quantized_image -- a numpy array of integer type
... | Calculates co-occurrence matrices for all the objects in the image.
Return an array P of shape (nobjects, nlevels, nlevels) such that
P[o, :, :] is the cooccurence matrix for object o.
quantized_image -- a numpy array of integer type
labels -- a numpy array of integer type
scale ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L35-L95 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H3 | def H3(self):
"Correlation."
multiplied = np.dot(self.levels[:, np.newaxis] + 1,
self.levels[np.newaxis] + 1)
repeated = np.tile(multiplied[np.newaxis], (self.nobjects, 1, 1))
summed = (repeated * self.P).sum(2).sum(1)
h3 = (summed - self.mux * self.mu... | python | def H3(self):
"Correlation."
multiplied = np.dot(self.levels[:, np.newaxis] + 1,
self.levels[np.newaxis] + 1)
repeated = np.tile(multiplied[np.newaxis], (self.nobjects, 1, 1))
summed = (repeated * self.P).sum(2).sum(1)
h3 = (summed - self.mux * self.mu... | Correlation. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L170-L178 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H5 | def H5(self):
"Inverse difference moment."
t = 1 + toeplitz(self.levels) ** 2
repeated = np.tile(t[np.newaxis], (self.nobjects, 1, 1))
return (1.0 / repeated * self.P).sum(2).sum(1) | python | def H5(self):
"Inverse difference moment."
t = 1 + toeplitz(self.levels) ** 2
repeated = np.tile(t[np.newaxis], (self.nobjects, 1, 1))
return (1.0 / repeated * self.P).sum(2).sum(1) | Inverse difference moment. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L184-L188 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H6 | def H6(self):
"Sum average."
if not hasattr(self, '_H6'):
self._H6 = ((self.rlevels2 + 2) * self.p_xplusy).sum(1)
return self._H6 | python | def H6(self):
"Sum average."
if not hasattr(self, '_H6'):
self._H6 = ((self.rlevels2 + 2) * self.p_xplusy).sum(1)
return self._H6 | Sum average. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L190-L194 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H7 | def H7(self):
"Sum variance (error in Haralick's original paper here)."
h6 = np.tile(self.H6(), (self.rlevels2.shape[1], 1)).transpose()
return (((self.rlevels2 + 2) - h6) ** 2 * self.p_xplusy).sum(1) | python | def H7(self):
"Sum variance (error in Haralick's original paper here)."
h6 = np.tile(self.H6(), (self.rlevels2.shape[1], 1)).transpose()
return (((self.rlevels2 + 2) - h6) ** 2 * self.p_xplusy).sum(1) | Sum variance (error in Haralick's original paper here). | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L196-L199 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H8 | def H8(self):
"Sum entropy."
return -(self.p_xplusy * np.log(self.p_xplusy + self.eps)).sum(1) | python | def H8(self):
"Sum entropy."
return -(self.p_xplusy * np.log(self.p_xplusy + self.eps)).sum(1) | Sum entropy. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L201-L203 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H9 | def H9(self):
"Entropy."
if not hasattr(self, '_H9'):
self._H9 = -(self.P * np.log(self.P + self.eps)).sum(2).sum(1)
return self._H9 | python | def H9(self):
"Entropy."
if not hasattr(self, '_H9'):
self._H9 = -(self.P * np.log(self.P + self.eps)).sum(2).sum(1)
return self._H9 | Entropy. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L205-L209 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H10 | def H10(self):
"Difference variance."
c = (self.rlevels * self.p_xminusy).sum(1)
c1 = np.tile(c, (self.nlevels,1)).transpose()
e = self.rlevels - c1
return (self.p_xminusy * e ** 2).sum(1) | python | def H10(self):
"Difference variance."
c = (self.rlevels * self.p_xminusy).sum(1)
c1 = np.tile(c, (self.nlevels,1)).transpose()
e = self.rlevels - c1
return (self.p_xminusy * e ** 2).sum(1) | Difference variance. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L211-L216 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H11 | def H11(self):
"Difference entropy."
return -(self.p_xminusy * np.log(self.p_xminusy + self.eps)).sum(1) | python | def H11(self):
"Difference entropy."
return -(self.p_xminusy * np.log(self.p_xminusy + self.eps)).sum(1) | Difference entropy. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L218-L220 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H12 | def H12(self):
"Information measure of correlation 1."
maxima = np.vstack((self.hx, self.hy)).max(0)
return (self.H9() - self.hxy1) / maxima | python | def H12(self):
"Information measure of correlation 1."
maxima = np.vstack((self.hx, self.hy)).max(0)
return (self.H9() - self.hxy1) / maxima | Information measure of correlation 1. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L222-L225 |
CellProfiler/centrosome | centrosome/haralick.py | Haralick.H13 | def H13(self):
"Information measure of correlation 2."
# An imaginary result has been encountered once in the Matlab
# version. The reason is unclear.
return np.sqrt(1 - np.exp(-2 * (self.hxy2 - self.H9()))) | python | def H13(self):
"Information measure of correlation 2."
# An imaginary result has been encountered once in the Matlab
# version. The reason is unclear.
return np.sqrt(1 - np.exp(-2 * (self.hxy2 - self.H9()))) | Information measure of correlation 2. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/haralick.py#L227-L231 |
CellProfiler/centrosome | centrosome/zernike.py | construct_zernike_lookuptable | def construct_zernike_lookuptable(zernike_indexes):
"""Return a lookup table of the sum-of-factorial part of the radial
polynomial of the zernike indexes passed
zernike_indexes - an Nx2 array of the Zernike polynomials to be
computed.
"""
n_max = np.max(zernike_indexes[:,0... | python | def construct_zernike_lookuptable(zernike_indexes):
"""Return a lookup table of the sum-of-factorial part of the radial
polynomial of the zernike indexes passed
zernike_indexes - an Nx2 array of the Zernike polynomials to be
computed.
"""
n_max = np.max(zernike_indexes[:,0... | Return a lookup table of the sum-of-factorial part of the radial
polynomial of the zernike indexes passed
zernike_indexes - an Nx2 array of the Zernike polynomials to be
computed. | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/zernike.py#L13-L34 |
CellProfiler/centrosome | centrosome/zernike.py | construct_zernike_polynomials | def construct_zernike_polynomials(x, y, zernike_indexes, mask=None, weight=None):
"""Return the zerike polynomials for all objects in an image
x - the X distance of a point from the center of its object
y - the Y distance of a point from the center of its object
zernike_indexes - an Nx2 array of th... | python | def construct_zernike_polynomials(x, y, zernike_indexes, mask=None, weight=None):
"""Return the zerike polynomials for all objects in an image
x - the X distance of a point from the center of its object
y - the Y distance of a point from the center of its object
zernike_indexes - an Nx2 array of th... | Return the zerike polynomials for all objects in an image
x - the X distance of a point from the center of its object
y - the Y distance of a point from the center of its object
zernike_indexes - an Nx2 array of the Zernike polynomials to be computed.
mask - a mask with same shape as X and Y of the... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/zernike.py#L37-L101 |
CellProfiler/centrosome | centrosome/zernike.py | score_zernike | def score_zernike(zf, radii, labels, indexes=None):
"""Score the output of construct_zernike_polynomials
zf - the output of construct_zernike_polynomials which is I x J x K
where K is the number of zernike polynomials computed
radii - a vector of the radius of each of N labeled objects
lab... | python | def score_zernike(zf, radii, labels, indexes=None):
"""Score the output of construct_zernike_polynomials
zf - the output of construct_zernike_polynomials which is I x J x K
where K is the number of zernike polynomials computed
radii - a vector of the radius of each of N labeled objects
lab... | Score the output of construct_zernike_polynomials
zf - the output of construct_zernike_polynomials which is I x J x K
where K is the number of zernike polynomials computed
radii - a vector of the radius of each of N labeled objects
labels - a label matrix
outputs a N x K matrix of the... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/zernike.py#L104-L141 |
CellProfiler/centrosome | centrosome/zernike.py | zernike | def zernike(zernike_indexes,labels,indexes):
"""Compute the Zernike features for the labels with the label #s in indexes
returns the score per labels and an array of one image per zernike feature
"""
#
# "Reverse_indexes" is -1 if a label # is not to be processed. Otherwise
# reverse_index[... | python | def zernike(zernike_indexes,labels,indexes):
"""Compute the Zernike features for the labels with the label #s in indexes
returns the score per labels and an array of one image per zernike feature
"""
#
# "Reverse_indexes" is -1 if a label # is not to be processed. Otherwise
# reverse_index[... | Compute the Zernike features for the labels with the label #s in indexes
returns the score per labels and an array of one image per zernike feature | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/zernike.py#L143-L192 |
CellProfiler/centrosome | centrosome/zernike.py | get_zernike_indexes | def get_zernike_indexes(limit=10):
"""Return a list of all Zernike indexes up to the given limit
limit - return all Zernike indexes with N less than this limit
returns an array of 2-tuples. Each tuple is organized as (N,M).
The Zernikes are stored as complex numbers with the real part
bein... | python | def get_zernike_indexes(limit=10):
"""Return a list of all Zernike indexes up to the given limit
limit - return all Zernike indexes with N less than this limit
returns an array of 2-tuples. Each tuple is organized as (N,M).
The Zernikes are stored as complex numbers with the real part
bein... | Return a list of all Zernike indexes up to the given limit
limit - return all Zernike indexes with N less than this limit
returns an array of 2-tuples. Each tuple is organized as (N,M).
The Zernikes are stored as complex numbers with the real part
being (N,M) and the imaginary being (N,-M) | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/zernike.py#L194-L211 |
CellProfiler/centrosome | centrosome/propagate.py | propagate | def propagate(image, labels, mask, weight):
"""Propagate the labels to the nearest pixels
image - gives the Z height when computing distance
labels - the labeled image pixels
mask - only label pixels within the mask
weight - the weighting of x/y distance vs z distance
high number... | python | def propagate(image, labels, mask, weight):
"""Propagate the labels to the nearest pixels
image - gives the Z height when computing distance
labels - the labeled image pixels
mask - only label pixels within the mask
weight - the weighting of x/y distance vs z distance
high number... | Propagate the labels to the nearest pixels
image - gives the Z height when computing distance
labels - the labeled image pixels
mask - only label pixels within the mask
weight - the weighting of x/y distance vs z distance
high numbers favor x/y, low favor z
returns a label m... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/propagate.py#L6-L31 |
CellProfiler/centrosome | centrosome/lapjv.py | lapjv | def lapjv(i, j, costs, wants_dual_variables = False, augmenting_row_reductions = 2):
'''Sparse linear assignment solution using Jonker-Volgenant algorithm
i,j - similarly-sized vectors that pair the object at index i[n] with
the object at index j[j]
costs - a vector of similar size... | python | def lapjv(i, j, costs, wants_dual_variables = False, augmenting_row_reductions = 2):
'''Sparse linear assignment solution using Jonker-Volgenant algorithm
i,j - similarly-sized vectors that pair the object at index i[n] with
the object at index j[j]
costs - a vector of similar size... | Sparse linear assignment solution using Jonker-Volgenant algorithm
i,j - similarly-sized vectors that pair the object at index i[n] with
the object at index j[j]
costs - a vector of similar size to i and j that is the cost of pairing
i[n] with j[n].
wants_d... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/lapjv.py#L10-L134 |
CellProfiler/centrosome | centrosome/lapjv.py | slow_reduction_transfer | def slow_reduction_transfer(ii, j, idx, count, x, u, v, c):
'''Perform the reduction transfer step from the Jonker-Volgenant algorithm
The data is input in a ragged array in terms of "i" structured as a
vector of values for each i,j combination where:
ii - the i to be reduced
j - the j-ind... | python | def slow_reduction_transfer(ii, j, idx, count, x, u, v, c):
'''Perform the reduction transfer step from the Jonker-Volgenant algorithm
The data is input in a ragged array in terms of "i" structured as a
vector of values for each i,j combination where:
ii - the i to be reduced
j - the j-ind... | Perform the reduction transfer step from the Jonker-Volgenant algorithm
The data is input in a ragged array in terms of "i" structured as a
vector of values for each i,j combination where:
ii - the i to be reduced
j - the j-index of every entry
idx - the index of the first entry for each i... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/lapjv.py#L136-L170 |
CellProfiler/centrosome | centrosome/lapjv.py | slow_augmenting_row_reduction | def slow_augmenting_row_reduction(n, ii, jj, idx, count, x, y, u, v, c):
'''Perform the augmenting row reduction step from the Jonker-Volgenaut algorithm
n - the number of i and j in the linear assignment problem
ii - the unassigned i
jj - the j-index of every entry in c
idx - the index of the ... | python | def slow_augmenting_row_reduction(n, ii, jj, idx, count, x, y, u, v, c):
'''Perform the augmenting row reduction step from the Jonker-Volgenaut algorithm
n - the number of i and j in the linear assignment problem
ii - the unassigned i
jj - the j-index of every entry in c
idx - the index of the ... | Perform the augmenting row reduction step from the Jonker-Volgenaut algorithm
n - the number of i and j in the linear assignment problem
ii - the unassigned i
jj - the j-index of every entry in c
idx - the index of the first entry for each i
count - the number of entries for each i
x - the ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/lapjv.py#L172-L235 |
CellProfiler/centrosome | centrosome/lapjv.py | slow_augment | def slow_augment(n, ii, jj, idx, count, x, y, u, v, c):
'''Perform the augmentation step to assign unassigned i and j
n - the # of i and j, also the marker of unassigned x and y
ii - the unassigned i
jj - the ragged arrays of j for each i
idx - the index of the first j for each i
count - th... | python | def slow_augment(n, ii, jj, idx, count, x, y, u, v, c):
'''Perform the augmentation step to assign unassigned i and j
n - the # of i and j, also the marker of unassigned x and y
ii - the unassigned i
jj - the ragged arrays of j for each i
idx - the index of the first j for each i
count - th... | Perform the augmentation step to assign unassigned i and j
n - the # of i and j, also the marker of unassigned x and y
ii - the unassigned i
jj - the ragged arrays of j for each i
idx - the index of the first j for each i
count - the number of j for each i
x - the assignments of j for each ... | https://github.com/CellProfiler/centrosome/blob/7bd9350a2d4ae1b215b81eabcecfe560bbb1f32a/centrosome/lapjv.py#L237-L360 |
koszullab/instaGRAAL | instagraal/cuda_lib_gl_single.py | sampler.estimate_parameters_rippe | def estimate_parameters_rippe(
self, max_dist_kb, size_bin_kb, display_graph
):
"""
estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb:
"""
logger.info("estimation of the paramete... | python | def estimate_parameters_rippe(
self, max_dist_kb, size_bin_kb, display_graph
):
"""
estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb:
"""
logger.info("estimation of the paramete... | estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb: | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/cuda_lib_gl_single.py#L2729-L2901 |
koszullab/instaGRAAL | instagraal/cuda_lib_gl_single.py | sampler.estimate_parameters | def estimate_parameters(self, max_dist_kb, size_bin_kb, display_graph):
"""
estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb:
"""
logger.info("estimation of the parameters of the model")
... | python | def estimate_parameters(self, max_dist_kb, size_bin_kb, display_graph):
"""
estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb:
"""
logger.info("estimation of the parameters of the model")
... | estimation by least square optimization of Rippe parameters on the
experimental data
:param max_dist_kb:
:param size_bin_kb: | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/cuda_lib_gl_single.py#L2903-L3021 |
koszullab/instaGRAAL | instagraal/linkage.py | collapse_degenerate_markers | def collapse_degenerate_markers(linkage_records):
"""Group all markers with no genetic distance as distinct features
to generate a BED file with.
Simple example with sixteen degenerate markers:
>>> marker_features = [
... ['36915_sctg_207_31842', 1, 0, 207, 31842],
... ['36941_sct... | python | def collapse_degenerate_markers(linkage_records):
"""Group all markers with no genetic distance as distinct features
to generate a BED file with.
Simple example with sixteen degenerate markers:
>>> marker_features = [
... ['36915_sctg_207_31842', 1, 0, 207, 31842],
... ['36941_sct... | Group all markers with no genetic distance as distinct features
to generate a BED file with.
Simple example with sixteen degenerate markers:
>>> marker_features = [
... ['36915_sctg_207_31842', 1, 0, 207, 31842],
... ['36941_sctg_207_61615', 1, 0, 207, 61615],
... ['36956_sctg_... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/linkage.py#L36-L123 |
koszullab/instaGRAAL | instagraal/linkage.py | linkage_group_ordering | def linkage_group_ordering(linkage_records):
"""Convert degenerate linkage records into ordered info_frags-like records
for comparison purposes.
Simple example:
>>> linkage_records = [
... ['linkage_group_1', 31842, 94039, 'sctg_207'],
... ['linkage_group_1', 95303, 95303, 'sctg_20... | python | def linkage_group_ordering(linkage_records):
"""Convert degenerate linkage records into ordered info_frags-like records
for comparison purposes.
Simple example:
>>> linkage_records = [
... ['linkage_group_1', 31842, 94039, 'sctg_207'],
... ['linkage_group_1', 95303, 95303, 'sctg_20... | Convert degenerate linkage records into ordered info_frags-like records
for comparison purposes.
Simple example:
>>> linkage_records = [
... ['linkage_group_1', 31842, 94039, 'sctg_207'],
... ['linkage_group_1', 95303, 95303, 'sctg_207'],
... ['linkage_group_2', 15892, 25865, '... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/linkage.py#L133-L187 |
koszullab/instaGRAAL | instagraal/linkage.py | compare_orderings | def compare_orderings(info_frags_records, linkage_orderings):
"""Given linkage groups and info_frags records, link pseudo-chromosomes to
scaffolds based on the initial contig composition of each group. Because
info_frags records are usually richer and may contain contigs not found
in linkage groups, th... | python | def compare_orderings(info_frags_records, linkage_orderings):
"""Given linkage groups and info_frags records, link pseudo-chromosomes to
scaffolds based on the initial contig composition of each group. Because
info_frags records are usually richer and may contain contigs not found
in linkage groups, th... | Given linkage groups and info_frags records, link pseudo-chromosomes to
scaffolds based on the initial contig composition of each group. Because
info_frags records are usually richer and may contain contigs not found
in linkage groups, those extra sequences are discarded.
Example with two linkage group... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/linkage.py#L190-L287 |
koszullab/instaGRAAL | instagraal/linkage.py | get_missing_blocks | def get_missing_blocks(info_frags_records, matching_pairs, linkage_orderings):
"""Get missing blocks in a scaffold based on the genetic map order.
Given matching scaffold blocks/genetic map blocks (based on restriction
sites and SNP markers, respectively), move around the scaffold blocks
such that the... | python | def get_missing_blocks(info_frags_records, matching_pairs, linkage_orderings):
"""Get missing blocks in a scaffold based on the genetic map order.
Given matching scaffold blocks/genetic map blocks (based on restriction
sites and SNP markers, respectively), move around the scaffold blocks
such that the... | Get missing blocks in a scaffold based on the genetic map order.
Given matching scaffold blocks/genetic map blocks (based on restriction
sites and SNP markers, respectively), move around the scaffold blocks
such that they map the genetic map order.
Parameters
----------
info_frags_records : d... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/linkage.py#L290-L435 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | parse_info_frags | def parse_info_frags(info_frags):
"""Import an info_frags.txt file and return a dictionary where each key
is a newly formed scaffold and each value is the list of bins and their
origin on the initial scaffolding.
"""
new_scaffolds = {}
with open(info_frags, "r") as info_frags_handle:
cu... | python | def parse_info_frags(info_frags):
"""Import an info_frags.txt file and return a dictionary where each key
is a newly formed scaffold and each value is the list of bins and their
origin on the initial scaffolding.
"""
new_scaffolds = {}
with open(info_frags, "r") as info_frags_handle:
cu... | Import an info_frags.txt file and return a dictionary where each key
is a newly formed scaffold and each value is the list of bins and their
origin on the initial scaffolding. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L39-L68 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | parse_bed | def parse_bed(bed_file):
"""Import a BED file (where the data entries are analogous to what may be
expected in an info_frags.txt file) and return a scaffold dictionary,
similarly to parse_info_frags.
"""
new_scaffolds = {}
with open(bed_file) as bed_handle:
for line in bed_handle:
... | python | def parse_bed(bed_file):
"""Import a BED file (where the data entries are analogous to what may be
expected in an info_frags.txt file) and return a scaffold dictionary,
similarly to parse_info_frags.
"""
new_scaffolds = {}
with open(bed_file) as bed_handle:
for line in bed_handle:
... | Import a BED file (where the data entries are analogous to what may be
expected in an info_frags.txt file) and return a scaffold dictionary,
similarly to parse_info_frags. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L73-L100 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | correct_scaffolds | def correct_scaffolds(scaffolds, corrector):
"""Unfinished
"""
new_scaffolds = {}
def are_overlapping(bin1, bin2):
"""Check for overlapping regions between two regions - necessary
requirement before potentially merging
"""
if bin2 is None:
return False
... | python | def correct_scaffolds(scaffolds, corrector):
"""Unfinished
"""
new_scaffolds = {}
def are_overlapping(bin1, bin2):
"""Check for overlapping regions between two regions - necessary
requirement before potentially merging
"""
if bin2 is None:
return False
... | Unfinished | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L103-L179 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | format_info_frags | def format_info_frags(info_frags):
"""A function to seamlessly run on either scaffold dictionaries or
info_frags.txt files without having to check the input first.
"""
if isinstance(info_frags, dict):
return info_frags
else:
try:
scaffolds = parse_info_frags(info_frags)
... | python | def format_info_frags(info_frags):
"""A function to seamlessly run on either scaffold dictionaries or
info_frags.txt files without having to check the input first.
"""
if isinstance(info_frags, dict):
return info_frags
else:
try:
scaffolds = parse_info_frags(info_frags)
... | A function to seamlessly run on either scaffold dictionaries or
info_frags.txt files without having to check the input first. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L182-L194 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | plot_info_frags | def plot_info_frags(scaffolds):
"""A crude way to visualize new scaffolds according to their origin on the
initial scaffolding. Each scaffold spawns a new plot. Orientations are
represented by different colors.
"""
scaffolds = format_info_frags(scaffolds)
for name, scaffold in scaffolds.items(... | python | def plot_info_frags(scaffolds):
"""A crude way to visualize new scaffolds according to their origin on the
initial scaffolding. Each scaffold spawns a new plot. Orientations are
represented by different colors.
"""
scaffolds = format_info_frags(scaffolds)
for name, scaffold in scaffolds.items(... | A crude way to visualize new scaffolds according to their origin on the
initial scaffolding. Each scaffold spawns a new plot. Orientations are
represented by different colors. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L197-L221 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | remove_spurious_insertions | def remove_spurious_insertions(scaffolds):
"""Remove all bins whose left and right neighbors belong to the same,
different scaffold.
Example with three such insertions in two different scaffolds:
>>> scaffolds = {
... "scaffold1": [
... ["contig1", 0, 0, 100, 1],
... | python | def remove_spurious_insertions(scaffolds):
"""Remove all bins whose left and right neighbors belong to the same,
different scaffold.
Example with three such insertions in two different scaffolds:
>>> scaffolds = {
... "scaffold1": [
... ["contig1", 0, 0, 100, 1],
... | Remove all bins whose left and right neighbors belong to the same,
different scaffold.
Example with three such insertions in two different scaffolds:
>>> scaffolds = {
... "scaffold1": [
... ["contig1", 0, 0, 100, 1],
... ["contig1", 1, 100, 200, 1],
... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L224-L301 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | correct_spurious_inversions | def correct_spurious_inversions(scaffolds, criterion="colinear"):
"""Invert bins based on orientation neighborhoods. Neighborhoods can be
defined by three criteria:
-a 'cis' neighborhood is a group of bins belonging to the same initial
contig
-a 'colinear' neighborhood is a 'cis' neighborhood where... | python | def correct_spurious_inversions(scaffolds, criterion="colinear"):
"""Invert bins based on orientation neighborhoods. Neighborhoods can be
defined by three criteria:
-a 'cis' neighborhood is a group of bins belonging to the same initial
contig
-a 'colinear' neighborhood is a 'cis' neighborhood where... | Invert bins based on orientation neighborhoods. Neighborhoods can be
defined by three criteria:
-a 'cis' neighborhood is a group of bins belonging to the same initial
contig
-a 'colinear' neighborhood is a 'cis' neighborhood where bins are
ordered the same way they were on the initial contig
-a... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L304-L462 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | rearrange_intra_scaffolds | def rearrange_intra_scaffolds(scaffolds):
"""Rearranges all bins within each scaffold such that all bins belonging
to the same initial contig are grouped together in the same order. When
two such groups are found, the smaller one is moved to the larger one.
"""
scaffolds = format_info_frags(scaffo... | python | def rearrange_intra_scaffolds(scaffolds):
"""Rearranges all bins within each scaffold such that all bins belonging
to the same initial contig are grouped together in the same order. When
two such groups are found, the smaller one is moved to the larger one.
"""
scaffolds = format_info_frags(scaffo... | Rearranges all bins within each scaffold such that all bins belonging
to the same initial contig are grouped together in the same order. When
two such groups are found, the smaller one is moved to the larger one. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L465-L508 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | write_fasta | def write_fasta(
init_fasta, info_frags, output=DEFAULT_NEW_GENOME_NAME, junction=False
):
"""Convert an info_frags.txt file into a fasta file given a reference.
Optionally adds junction sequences to reflect the possibly missing base
pairs between two newly joined scaffolds.
"""
init_genome = ... | python | def write_fasta(
init_fasta, info_frags, output=DEFAULT_NEW_GENOME_NAME, junction=False
):
"""Convert an info_frags.txt file into a fasta file given a reference.
Optionally adds junction sequences to reflect the possibly missing base
pairs between two newly joined scaffolds.
"""
init_genome = ... | Convert an info_frags.txt file into a fasta file given a reference.
Optionally adds junction sequences to reflect the possibly missing base
pairs between two newly joined scaffolds. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L604-L664 |
koszullab/instaGRAAL | instagraal/parse_info_frags.py | is_block | def is_block(bin_list):
"""Check if a bin list has exclusively consecutive bin ids.
"""
id_set = set((my_bin[1] for my_bin in bin_list))
start_id, end_id = min(id_set), max(id_set)
return id_set == set(range(start_id, end_id + 1)) | python | def is_block(bin_list):
"""Check if a bin list has exclusively consecutive bin ids.
"""
id_set = set((my_bin[1] for my_bin in bin_list))
start_id, end_id = min(id_set), max(id_set)
return id_set == set(range(start_id, end_id + 1)) | Check if a bin list has exclusively consecutive bin ids. | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/parse_info_frags.py#L804-L810 |
koszullab/instaGRAAL | instagraal/leastsqbound.py | internal2external_grad | def internal2external_grad(xi, bounds):
"""
Calculate the internal to external gradiant
Calculates the partial of external over internal
"""
ge = np.empty_like(xi)
for i, (v, bound) in enumerate(zip(xi, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
... | python | def internal2external_grad(xi, bounds):
"""
Calculate the internal to external gradiant
Calculates the partial of external over internal
"""
ge = np.empty_like(xi)
for i, (v, bound) in enumerate(zip(xi, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
... | Calculate the internal to external gradiant
Calculates the partial of external over internal | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/leastsqbound.py#L19-L46 |
koszullab/instaGRAAL | instagraal/leastsqbound.py | internal2external | def internal2external(xi, bounds):
""" Convert a series of internal variables to external variables"""
xe = np.empty_like(xi)
for i, (v, bound) in enumerate(zip(xi, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
if a == None and b == None: # No constraints
... | python | def internal2external(xi, bounds):
""" Convert a series of internal variables to external variables"""
xe = np.empty_like(xi)
for i, (v, bound) in enumerate(zip(xi, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
if a == None and b == None: # No constraints
... | Convert a series of internal variables to external variables | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/leastsqbound.py#L56-L78 |
koszullab/instaGRAAL | instagraal/leastsqbound.py | external2internal | def external2internal(xe, bounds):
""" Convert a series of external variables to internal variables"""
xi = np.empty_like(xe)
for i, (v, bound) in enumerate(zip(xe, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
if a == None and b == None: # No constraints
... | python | def external2internal(xe, bounds):
""" Convert a series of external variables to internal variables"""
xi = np.empty_like(xe)
for i, (v, bound) in enumerate(zip(xe, bounds)):
a = bound[0] # minimum
b = bound[1] # maximum
if a == None and b == None: # No constraints
... | Convert a series of external variables to internal variables | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/leastsqbound.py#L81-L103 |
koszullab/instaGRAAL | instagraal/leastsqbound.py | calc_cov_x | def calc_cov_x(infodic, p):
"""
Calculate cov_x from fjac, ipvt and p as is done in leastsq
"""
fjac = infodic["fjac"]
ipvt = infodic["ipvt"]
n = len(p)
# adapted from leastsq function in scipy/optimize/minpack.py
perm = np.take(np.eye(n), ipvt - 1, 0)
r = np.triu(np.transpose(fjac... | python | def calc_cov_x(infodic, p):
"""
Calculate cov_x from fjac, ipvt and p as is done in leastsq
"""
fjac = infodic["fjac"]
ipvt = infodic["ipvt"]
n = len(p)
# adapted from leastsq function in scipy/optimize/minpack.py
perm = np.take(np.eye(n), ipvt - 1, 0)
r = np.triu(np.transpose(fjac... | Calculate cov_x from fjac, ipvt and p as is done in leastsq | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/leastsqbound.py#L112-L129 |
koszullab/instaGRAAL | instagraal/leastsqbound.py | leastsqbound | def leastsqbound(func, x0, bounds, args=(), **kw):
"""
Constrained multivariant Levenberg-Marquard optimization
Minimize the sum of squares of a given function using the
Levenberg-Marquard algorithm. Contraints on parameters are inforced using
variable transformations as described in the MINUIT U... | python | def leastsqbound(func, x0, bounds, args=(), **kw):
"""
Constrained multivariant Levenberg-Marquard optimization
Minimize the sum of squares of a given function using the
Levenberg-Marquard algorithm. Contraints on parameters are inforced using
variable transformations as described in the MINUIT U... | Constrained multivariant Levenberg-Marquard optimization
Minimize the sum of squares of a given function using the
Levenberg-Marquard algorithm. Contraints on parameters are inforced using
variable transformations as described in the MINUIT User's Guide by
Fred James and Matthias Winkler.
Parame... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/leastsqbound.py#L132-L183 |
guykisel/inline-plz | inlineplz/interfaces/github.py | GitHubInterface.start_review | def start_review(self):
"""Mark our review as started."""
if self.set_status:
self.github_repo.create_status(
state="pending",
description="Static analysis in progress.",
context="inline-plz",
sha=self.last_sha,
) | python | def start_review(self):
"""Mark our review as started."""
if self.set_status:
self.github_repo.create_status(
state="pending",
description="Static analysis in progress.",
context="inline-plz",
sha=self.last_sha,
) | Mark our review as started. | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/interfaces/github.py#L199-L207 |
guykisel/inline-plz | inlineplz/interfaces/github.py | GitHubInterface.finish_review | def finish_review(self, success=True, error=False):
"""Mark our review as finished."""
if self.set_status:
if error:
self.github_repo.create_status(
state="error",
description="Static analysis error! inline-plz failed to run.",
... | python | def finish_review(self, success=True, error=False):
"""Mark our review as finished."""
if self.set_status:
if error:
self.github_repo.create_status(
state="error",
description="Static analysis error! inline-plz failed to run.",
... | Mark our review as finished. | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/interfaces/github.py#L209-L232 |
guykisel/inline-plz | inlineplz/interfaces/github.py | GitHubInterface.out_of_date | def out_of_date(self):
"""Check if our local latest sha matches the remote latest sha"""
try:
latest_remote_sha = self.pr_commits(self.pull_request.refresh(True))[-1].sha
print("Latest remote sha: {}".format(latest_remote_sha))
try:
print("Ratelimit re... | python | def out_of_date(self):
"""Check if our local latest sha matches the remote latest sha"""
try:
latest_remote_sha = self.pr_commits(self.pull_request.refresh(True))[-1].sha
print("Latest remote sha: {}".format(latest_remote_sha))
try:
print("Ratelimit re... | Check if our local latest sha matches the remote latest sha | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/interfaces/github.py#L234-L245 |
guykisel/inline-plz | inlineplz/interfaces/github.py | GitHubInterface.position | def position(self, message):
"""Calculate position within the PR, which is not the line number"""
if not message.line_number:
message.line_number = 1
for patched_file in self.patch:
target = patched_file.target_file.lstrip("b/")
if target == message.path:
... | python | def position(self, message):
"""Calculate position within the PR, which is not the line number"""
if not message.line_number:
message.line_number = 1
for patched_file in self.patch:
target = patched_file.target_file.lstrip("b/")
if target == message.path:
... | Calculate position within the PR, which is not the line number | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/interfaces/github.py#L444-L461 |
koszullab/instaGRAAL | instagraal/simu_single.py | simulation.modify_vect_frags | def modify_vect_frags(self):
"include repeated frags"
modified_vect_frags = dict()
init_vect_frags = self.level.S_o_A_frags
# init_max_id_d = init_vect_frags["id"].max()
max_id_F = len(init_vect_frags["id"])
max_id_C = init_vect_frags["id_c"].max() + 1
# HSV_tu... | python | def modify_vect_frags(self):
"include repeated frags"
modified_vect_frags = dict()
init_vect_frags = self.level.S_o_A_frags
# init_max_id_d = init_vect_frags["id"].max()
max_id_F = len(init_vect_frags["id"])
max_id_C = init_vect_frags["id_c"].max() + 1
# HSV_tu... | include repeated frags | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/simu_single.py#L261-L450 |
koszullab/instaGRAAL | instagraal/simu_single.py | simulation.modify_sub_vect_frags | def modify_sub_vect_frags(self):
"include repeated frags"
modified_vect_frags = dict()
init_vect_frags = self.sub_level.S_o_A_frags
# init_max_id_d = init_vect_frags["id"].max()
max_id_F = len(init_vect_frags["id"])
max_id_C = init_vect_frags["id_c"].max() + 1
#... | python | def modify_sub_vect_frags(self):
"include repeated frags"
modified_vect_frags = dict()
init_vect_frags = self.sub_level.S_o_A_frags
# init_max_id_d = init_vect_frags["id"].max()
max_id_F = len(init_vect_frags["id"])
max_id_C = init_vect_frags["id_c"].max() + 1
#... | include repeated frags | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/simu_single.py#L452-L637 |
koszullab/instaGRAAL | instagraal/instagraal.py | window.draw | def draw(self):
"""Render the particles"""
# update or particle positions by calling the OpenCL kernel
# self.cle.execute(10)
OpenGL.GL.glFlush()
OpenGL.GL.glClear(
OpenGL.GL.GL_COLOR_BUFFER_BIT | OpenGL.GL.GL_DEPTH_BUFFER_BIT
)
if self.white == -1:
... | python | def draw(self):
"""Render the particles"""
# update or particle positions by calling the OpenCL kernel
# self.cle.execute(10)
OpenGL.GL.glFlush()
OpenGL.GL.glClear(
OpenGL.GL.GL_COLOR_BUFFER_BIT | OpenGL.GL.GL_DEPTH_BUFFER_BIT
)
if self.white == -1:
... | Render the particles | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/instagraal.py#L1564-L1772 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | build_and_filter | def build_and_filter(base_folder, size_pyramid, factor, thresh_factor=1):
"""Build a filtered pyramid of contact maps
Build a fragment pyramid for multi-scale analysis and remove high sparsity
(i.e. low-coverage) and short fragments.
Parameters
----------
base_folder : str or pathlib.Path
... | python | def build_and_filter(base_folder, size_pyramid, factor, thresh_factor=1):
"""Build a filtered pyramid of contact maps
Build a fragment pyramid for multi-scale analysis and remove high sparsity
(i.e. low-coverage) and short fragments.
Parameters
----------
base_folder : str or pathlib.Path
... | Build a filtered pyramid of contact maps
Build a fragment pyramid for multi-scale analysis and remove high sparsity
(i.e. low-coverage) and short fragments.
Parameters
----------
base_folder : str or pathlib.Path
Where to create the hdf5 files containing the matrices.
size_pyramid : i... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L29-L203 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | build | def build(base_folder, size_pyramid, factor, min_bin_per_contig):
"""Build a pyramid of contact maps
Build a fragment pyramid for multi-scale analysis
Parameters
----------
base_folder : str or pathlib.Path
Where to create the hdf5 files containing the matrices.
size_pyramid : int
... | python | def build(base_folder, size_pyramid, factor, min_bin_per_contig):
"""Build a pyramid of contact maps
Build a fragment pyramid for multi-scale analysis
Parameters
----------
base_folder : str or pathlib.Path
Where to create the hdf5 files containing the matrices.
size_pyramid : int
... | Build a pyramid of contact maps
Build a fragment pyramid for multi-scale analysis
Parameters
----------
base_folder : str or pathlib.Path
Where to create the hdf5 files containing the matrices.
size_pyramid : int
How many levels (contact maps of decreasing resolution) to genera... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L206-L329 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | abs_contact_2_coo_file | def abs_contact_2_coo_file(abs_contact_file, coo_file):
"""Convert contact maps between old-style and new-style formats.
A legacy function that converts contact maps from the older GRAAL format to
the simpler instaGRAAL format. This is useful with datasets generated by
Hi-C box.
Parameters
---... | python | def abs_contact_2_coo_file(abs_contact_file, coo_file):
"""Convert contact maps between old-style and new-style formats.
A legacy function that converts contact maps from the older GRAAL format to
the simpler instaGRAAL format. This is useful with datasets generated by
Hi-C box.
Parameters
---... | Convert contact maps between old-style and new-style formats.
A legacy function that converts contact maps from the older GRAAL format to
the simpler instaGRAAL format. This is useful with datasets generated by
Hi-C box.
Parameters
----------
abs_contact_file : str, file or pathlib.Path
... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L332-L381 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | fill_sparse_pyramid_level | def fill_sparse_pyramid_level(pyramid_handle, level, contact_file, nfrags):
"""Fill a level with sparse contact map data
Fill values from the simple text matrix file to the hdf5-based pyramid
level with contact data.
Parameters
----------
pyramid_handle : h5py.File
The hdf5 file ha... | python | def fill_sparse_pyramid_level(pyramid_handle, level, contact_file, nfrags):
"""Fill a level with sparse contact map data
Fill values from the simple text matrix file to the hdf5-based pyramid
level with contact data.
Parameters
----------
pyramid_handle : h5py.File
The hdf5 file ha... | Fill a level with sparse contact map data
Fill values from the simple text matrix file to the hdf5-based pyramid
level with contact data.
Parameters
----------
pyramid_handle : h5py.File
The hdf5 file handle containing the whole dataset.
level : int
The level (resolution) t... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L384-L450 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | init_frag_list | def init_frag_list(fragment_list, new_frag_list):
"""Adapt the original fragment list to fit the build function requirements
Parameters
----------
fragment_list : str, file or pathlib.Path
The input fragment list.
new_frag_list : str, file or pathlib.Path
The output fragment list to... | python | def init_frag_list(fragment_list, new_frag_list):
"""Adapt the original fragment list to fit the build function requirements
Parameters
----------
fragment_list : str, file or pathlib.Path
The input fragment list.
new_frag_list : str, file or pathlib.Path
The output fragment list to... | Adapt the original fragment list to fit the build function requirements
Parameters
----------
fragment_list : str, file or pathlib.Path
The input fragment list.
new_frag_list : str, file or pathlib.Path
The output fragment list to be written.
Returns
-------
i : int
... | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L453-L519 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | pyramid.zoom_in_frag | def zoom_in_frag(self, curr_frag):
"""
:param curr_frag:
"""
level = curr_frag[1]
frag = curr_frag[0]
output = []
if level > 0:
str_level = str(level)
sub_low = self.spec_level[str_level]["fragments_dict"][frag][
"sub_low_in... | python | def zoom_in_frag(self, curr_frag):
"""
:param curr_frag:
"""
level = curr_frag[1]
frag = curr_frag[0]
output = []
if level > 0:
str_level = str(level)
sub_low = self.spec_level[str_level]["fragments_dict"][frag][
"sub_low_in... | :param curr_frag: | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1697-L1717 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | pyramid.zoom_out_frag | def zoom_out_frag(self, curr_frag):
"""
:param curr_frag:
"""
level = curr_frag[1]
frag = curr_frag[0]
output = []
if level > 0:
str_level = str(level)
high_frag = self.spec_level[str_level]["fragments_dict"][frag][
"super_i... | python | def zoom_out_frag(self, curr_frag):
"""
:param curr_frag:
"""
level = curr_frag[1]
frag = curr_frag[0]
output = []
if level > 0:
str_level = str(level)
high_frag = self.spec_level[str_level]["fragments_dict"][frag][
"super_i... | :param curr_frag: | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1719-L1735 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | pyramid.zoom_in_pixel | def zoom_in_pixel(self, curr_pixel):
""" return the curr_frag at a higher resolution"""
low_frag = curr_pixel[0]
high_frag = curr_pixel[1]
level = curr_pixel[2]
if level > 0:
str_level = str(level)
low_sub_low = self.spec_level[str_level]["fragments_dict"]... | python | def zoom_in_pixel(self, curr_pixel):
""" return the curr_frag at a higher resolution"""
low_frag = curr_pixel[0]
high_frag = curr_pixel[1]
level = curr_pixel[2]
if level > 0:
str_level = str(level)
low_sub_low = self.spec_level[str_level]["fragments_dict"]... | return the curr_frag at a higher resolution | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1759-L1785 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | pyramid.zoom_out_pixel | def zoom_out_pixel(self, curr_pixel):
""" return the curr_frag at a lower resolution"""
low_frag = curr_pixel[0]
high_frag = curr_pixel[1]
level = curr_pixel[2]
str_level = str(level)
if level < self.n_level - 1:
low_super = self.spec_level[str_level]["fragmen... | python | def zoom_out_pixel(self, curr_pixel):
""" return the curr_frag at a lower resolution"""
low_frag = curr_pixel[0]
high_frag = curr_pixel[1]
level = curr_pixel[2]
str_level = str(level)
if level < self.n_level - 1:
low_super = self.spec_level[str_level]["fragmen... | return the curr_frag at a lower resolution | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1787-L1807 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | pyramid.zoom_in_area | def zoom_in_area(self, area):
""" zoom in area"""
x = area[0]
y = area[1]
level = x[2]
logger.debug("x = {}".format(x))
logger.debug("y = {}".format(y))
logger.debug("level = {}".format(level))
if level == y[2] and level > 0:
new_level = level ... | python | def zoom_in_area(self, area):
""" zoom in area"""
x = area[0]
y = area[1]
level = x[2]
logger.debug("x = {}".format(x))
logger.debug("y = {}".format(y))
logger.debug("level = {}".format(level))
if level == y[2] and level > 0:
new_level = level ... | zoom in area | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1809-L1835 |
koszullab/instaGRAAL | instagraal/pyramid_sparse.py | level.load_data | def load_data(self, pyramid):
"""
:param pyramid: hic pyramid
"""
import colorsys
logger.info("loading data from level = {}".format(self.level))
# self.im_init = np.array(pyramid.data[str(self.level)],
# dtype=np.int32)
# self.n_frags = self.im_init.shape... | python | def load_data(self, pyramid):
"""
:param pyramid: hic pyramid
"""
import colorsys
logger.info("loading data from level = {}".format(self.level))
# self.im_init = np.array(pyramid.data[str(self.level)],
# dtype=np.int32)
# self.n_frags = self.im_init.shape... | :param pyramid: hic pyramid | https://github.com/koszullab/instaGRAAL/blob/1c02ca838e57d8178eec79f223644b2acd0153dd/instagraal/pyramid_sparse.py#L1927-L2155 |
guykisel/inline-plz | inlineplz/main.py | load_config | def load_config(args, config_path=".inlineplz.yml"):
"""Load inline-plz config from yaml config file with reasonable defaults."""
config = {}
try:
with open(config_path) as configfile:
config = yaml.safe_load(configfile) or {}
if config:
print("Loaded config f... | python | def load_config(args, config_path=".inlineplz.yml"):
"""Load inline-plz config from yaml config file with reasonable defaults."""
config = {}
try:
with open(config_path) as configfile:
config = yaml.safe_load(configfile) or {}
if config:
print("Loaded config f... | Load inline-plz config from yaml config file with reasonable defaults. | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/main.py#L102-L143 |
guykisel/inline-plz | inlineplz/main.py | inline | def inline(args):
"""
Parse input file with the specified parser and post messages based on lint output
:param args: Contains the following
interface: How are we going to post comments?
owner: Username of repo owner
repo: Repository name
pr: Pull request ID
token: Au... | python | def inline(args):
"""
Parse input file with the specified parser and post messages based on lint output
:param args: Contains the following
interface: How are we going to post comments?
owner: Username of repo owner
repo: Repository name
pr: Pull request ID
token: Au... | Parse input file with the specified parser and post messages based on lint output
:param args: Contains the following
interface: How are we going to post comments?
owner: Username of repo owner
repo: Repository name
pr: Pull request ID
token: Authentication for repository
... | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/main.py#L146-L270 |
guykisel/inline-plz | inlineplz/linter_runner.py | LinterRunner.cleanup | def cleanup():
"""Delete standard installation directories."""
for install_dir in linters.INSTALL_DIRS:
try:
shutil.rmtree(install_dir, ignore_errors=True)
except Exception:
print(
"{0}\nFailed to delete {1}".format(
... | python | def cleanup():
"""Delete standard installation directories."""
for install_dir in linters.INSTALL_DIRS:
try:
shutil.rmtree(install_dir, ignore_errors=True)
except Exception:
print(
"{0}\nFailed to delete {1}".format(
... | Delete standard installation directories. | https://github.com/guykisel/inline-plz/blob/b5b1744e9156e31f68b519c0d8022feff79888ae/inlineplz/linter_runner.py#L167-L178 |
quantmind/aio-kong | kong/services.py | Services.apply_json | async def apply_json(self, data):
"""Apply a JSON data object for a service
"""
if not isinstance(data, list):
data = [data]
result = []
for entry in data:
if not isinstance(entry, dict):
raise KongError('dictionary required')
e... | python | async def apply_json(self, data):
"""Apply a JSON data object for a service
"""
if not isinstance(data, list):
data = [data]
result = []
for entry in data:
if not isinstance(entry, dict):
raise KongError('dictionary required')
e... | Apply a JSON data object for a service | https://github.com/quantmind/aio-kong/blob/65607c6a6fea4c50b94e5f06dfbcd2841dfa8abf/kong/services.py#L34-L67 |
quantmind/aio-kong | kong/snis.py | Snis.apply_json | async def apply_json(self, data):
"""Apply a JSON data object for a service
"""
if not isinstance(data, list):
data = [data]
result = []
for entry in data:
name = entry.pop('name')
if await self.has(name):
sni = await self.updat... | python | async def apply_json(self, data):
"""Apply a JSON data object for a service
"""
if not isinstance(data, list):
data = [data]
result = []
for entry in data:
name = entry.pop('name')
if await self.has(name):
sni = await self.updat... | Apply a JSON data object for a service | https://github.com/quantmind/aio-kong/blob/65607c6a6fea4c50b94e5f06dfbcd2841dfa8abf/kong/snis.py#L7-L20 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseVolume.resize | def resize(self, size):
"""
Resize the volume to the specified size (in GB).
"""
self.instance.resize_volume(size)
self.size = size | python | def resize(self, size):
"""
Resize the volume to the specified size (in GB).
"""
self.instance.resize_volume(size)
self.size = size | Resize the volume to the specified size (in GB). | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L53-L58 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager.get | def get(self, item):
"""
This additional code is necessary to properly return the 'volume'
attribute of the instance as a CloudDatabaseVolume object instead of
a raw dict.
"""
resource = super(CloudDatabaseManager, self).get(item)
resource.volume = CloudDatabaseVo... | python | def get(self, item):
"""
This additional code is necessary to properly return the 'volume'
attribute of the instance as a CloudDatabaseVolume object instead of
a raw dict.
"""
resource = super(CloudDatabaseManager, self).get(item)
resource.volume = CloudDatabaseVo... | This additional code is necessary to properly return the 'volume'
attribute of the instance as a CloudDatabaseVolume object instead of
a raw dict. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L73-L81 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager._create_body | def _create_body(self, name, flavor=None, volume=None, databases=None,
users=None, version=None, type=None):
"""
Used to create the dict required to create a Cloud Database instance.
"""
if flavor is None:
flavor = 1
flavor_ref = self.api._get_flavor_ref(f... | python | def _create_body(self, name, flavor=None, volume=None, databases=None,
users=None, version=None, type=None):
"""
Used to create the dict required to create a Cloud Database instance.
"""
if flavor is None:
flavor = 1
flavor_ref = self.api._get_flavor_ref(f... | Used to create the dict required to create a Cloud Database instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L84-L114 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager.create_backup | def create_backup(self, instance, name, description=None):
"""
Creates a backup of the specified instance, giving it the specified
name along with an optional description.
"""
body = {"backup": {
"instance": utils.get_id(instance),
"name": name,
... | python | def create_backup(self, instance, name, description=None):
"""
Creates a backup of the specified instance, giving it the specified
name along with an optional description.
"""
body = {"backup": {
"instance": utils.get_id(instance),
"name": name,
... | Creates a backup of the specified instance, giving it the specified
name along with an optional description. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L117-L131 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager.restore_backup | def restore_backup(self, backup, name, flavor, volume):
"""
Restores a backup to a new database instance. You must supply a backup
(either the ID or a CloudDatabaseBackup object), a name for the new
instance, as well as a flavor and volume size (in GB) for the instance.
"""
... | python | def restore_backup(self, backup, name, flavor, volume):
"""
Restores a backup to a new database instance. You must supply a backup
(either the ID or a CloudDatabaseBackup object), a name for the new
instance, as well as a flavor and volume size (in GB) for the instance.
"""
... | Restores a backup to a new database instance. You must supply a backup
(either the ID or a CloudDatabaseBackup object), a name for the new
instance, as well as a flavor and volume size (in GB) for the instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L134-L149 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager.list_backups | def list_backups(self, instance=None, marker=0, limit=20):
"""
Returns a paginated list of backups, or just for a particular
instance.
"""
return self.api._backup_manager.list(instance=instance, limit=limit,
marker=marker) | python | def list_backups(self, instance=None, marker=0, limit=20):
"""
Returns a paginated list of backups, or just for a particular
instance.
"""
return self.api._backup_manager.list(instance=instance, limit=limit,
marker=marker) | Returns a paginated list of backups, or just for a particular
instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L152-L158 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseManager._list_backups_for_instance | def _list_backups_for_instance(self, instance, marker=0, limit=20):
"""
Instance-specific backups are handled through the instance manager,
not the backup manager.
"""
uri = "/%s/%s/backups?limit=%d&marker=%d" % (self.uri_base,
... | python | def _list_backups_for_instance(self, instance, marker=0, limit=20):
"""
Instance-specific backups are handled through the instance manager,
not the backup manager.
"""
uri = "/%s/%s/backups?limit=%d&marker=%d" % (self.uri_base,
... | Instance-specific backups are handled through the instance manager,
not the backup manager. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L161-L173 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUserManager._get_db_names | def _get_db_names(self, dbs, strict=True):
"""
Accepts a single db (name or object) or a list of dbs, and returns a
list of database names. If any of the supplied dbs do not exist, a
NoSuchDatabase exception will be raised, unless you pass strict=False.
"""
dbs = utils.co... | python | def _get_db_names(self, dbs, strict=True):
"""
Accepts a single db (name or object) or a list of dbs, and returns a
list of database names. If any of the supplied dbs do not exist, a
NoSuchDatabase exception will be raised, unless you pass strict=False.
"""
dbs = utils.co... | Accepts a single db (name or object) or a list of dbs, and returns a
list of database names. If any of the supplied dbs do not exist, a
NoSuchDatabase exception will be raised, unless you pass strict=False. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L209-L226 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUserManager.update | def update(self, user, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
if not any((name, password, host)):
raise exc.MissingDBUserParameters("You must supply at least one of "
... | python | def update(self, user, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
if not any((name, password, host)):
raise exc.MissingDBUserParameters("You must supply at least one of "
... | Allows you to change one or more of the user's username, password, or
host. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L239-L264 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUserManager.list_user_access | def list_user_access(self, user):
"""
Returns a list of all database names for which the specified user
has access rights.
"""
user = utils.get_name(user)
uri = "/%s/%s/databases" % (self.uri_base, user)
try:
resp, resp_body = self.api.method_get(uri)
... | python | def list_user_access(self, user):
"""
Returns a list of all database names for which the specified user
has access rights.
"""
user = utils.get_name(user)
uri = "/%s/%s/databases" % (self.uri_base, user)
try:
resp, resp_body = self.api.method_get(uri)
... | Returns a list of all database names for which the specified user
has access rights. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L267-L279 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUserManager.grant_user_access | def grant_user_access(self, user, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user. You may
pass in either a single db or a list of dbs.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify ... | python | def grant_user_access(self, user, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user. You may
pass in either a single db or a list of dbs.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify ... | Gives access to the databases listed in `db_names` to the user. You may
pass in either a single db or a list of dbs.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify `strict=False` in the call. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L282-L298 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUserManager.revoke_user_access | def revoke_user_access(self, user, db_names, strict=True):
"""
Revokes access to the databases listed in `db_names` for the user.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify `strict=False` in the call.
"""
user = ut... | python | def revoke_user_access(self, user, db_names, strict=True):
"""
Revokes access to the databases listed in `db_names` for the user.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify `strict=False` in the call.
"""
user = ut... | Revokes access to the databases listed in `db_names` for the user.
If any of the databases do not exist, a NoSuchDatabase exception will
be raised, unless you specify `strict=False` in the call. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L301-L313 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseBackupManager.list | def list(self, instance=None, limit=20, marker=0):
"""
Return a paginated list of backups, or just for a particular
instance.
"""
if instance is None:
return super(CloudDatabaseBackupManager, self).list()
return self.api._manager._list_backups_for_instance(ins... | python | def list(self, instance=None, limit=20, marker=0):
"""
Return a paginated list of backups, or just for a particular
instance.
"""
if instance is None:
return super(CloudDatabaseBackupManager, self).list()
return self.api._manager._list_backups_for_instance(ins... | Return a paginated list of backups, or just for a particular
instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L331-L339 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.get | def get(self):
"""
Need to override the default get() behavior by making the 'volume'
attribute into a CloudDatabaseVolume object instead of the raw dict.
"""
super(CloudDatabaseInstance, self).get()
# Make the volume into an accessible object instead of a dict
se... | python | def get(self):
"""
Need to override the default get() behavior by making the 'volume'
attribute into a CloudDatabaseVolume object instead of the raw dict.
"""
super(CloudDatabaseInstance, self).get()
# Make the volume into an accessible object instead of a dict
se... | Need to override the default get() behavior by making the 'volume'
attribute into a CloudDatabaseVolume object instead of the raw dict. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L362-L369 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.list_databases | def list_databases(self, limit=None, marker=None):
"""Returns a list of the names of all databases for this instance."""
return self._database_manager.list(limit=limit, marker=marker) | python | def list_databases(self, limit=None, marker=None):
"""Returns a list of the names of all databases for this instance."""
return self._database_manager.list(limit=limit, marker=marker) | Returns a list of the names of all databases for this instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L372-L374 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.list_users | def list_users(self, limit=None, marker=None):
"""Returns a list of the names of all users for this instance."""
return self._user_manager.list(limit=limit, marker=marker) | python | def list_users(self, limit=None, marker=None):
"""Returns a list of the names of all users for this instance."""
return self._user_manager.list(limit=limit, marker=marker) | Returns a list of the names of all users for this instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L377-L379 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.get_user | def get_user(self, name):
"""
Finds the user in this instance with the specified name, and
returns a CloudDatabaseUser object. If no match is found, a
NoSuchDatabaseUser exception is raised.
"""
try:
return self._user_manager.get(name)
except exc.NotFo... | python | def get_user(self, name):
"""
Finds the user in this instance with the specified name, and
returns a CloudDatabaseUser object. If no match is found, a
NoSuchDatabaseUser exception is raised.
"""
try:
return self._user_manager.get(name)
except exc.NotFo... | Finds the user in this instance with the specified name, and
returns a CloudDatabaseUser object. If no match is found, a
NoSuchDatabaseUser exception is raised. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L382-L392 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.get_database | def get_database(self, name):
"""
Finds the database in this instance with the specified name, and
returns a CloudDatabaseDatabase object. If no match is found, a
NoSuchDatabase exception is raised.
"""
try:
return [db for db in self.list_databases()
... | python | def get_database(self, name):
"""
Finds the database in this instance with the specified name, and
returns a CloudDatabaseDatabase object. If no match is found, a
NoSuchDatabase exception is raised.
"""
try:
return [db for db in self.list_databases()
... | Finds the database in this instance with the specified name, and
returns a CloudDatabaseDatabase object. If no match is found, a
NoSuchDatabase exception is raised. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L395-L406 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.create_database | def create_database(self, name, character_set=None, collate=None):
"""
Creates a database with the specified name. If a database with
that name already exists, a BadRequest (400) exception will
be raised.
"""
if character_set is None:
character_set = "utf8"
... | python | def create_database(self, name, character_set=None, collate=None):
"""
Creates a database with the specified name. If a database with
that name already exists, a BadRequest (400) exception will
be raised.
"""
if character_set is None:
character_set = "utf8"
... | Creates a database with the specified name. If a database with
that name already exists, a BadRequest (400) exception will
be raised. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L409-L423 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.create_user | def create_user(self, name, password, database_names, host=None):
"""
Creates a user with the specified name and password, and gives that
user access to the specified database(s).
If a user with that name already exists, a BadRequest (400) exception
will be raised.
"""
... | python | def create_user(self, name, password, database_names, host=None):
"""
Creates a user with the specified name and password, and gives that
user access to the specified database(s).
If a user with that name already exists, a BadRequest (400) exception
will be raised.
"""
... | Creates a user with the specified name and password, and gives that
user access to the specified database(s).
If a user with that name already exists, a BadRequest (400) exception
will be raised. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L426-L443 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.delete_database | def delete_database(self, name_or_obj):
"""
Deletes the specified database. If no database by that name
exists, no exception will be raised; instead, nothing at all
is done.
"""
name = utils.get_name(name_or_obj)
self._database_manager.delete(name) | python | def delete_database(self, name_or_obj):
"""
Deletes the specified database. If no database by that name
exists, no exception will be raised; instead, nothing at all
is done.
"""
name = utils.get_name(name_or_obj)
self._database_manager.delete(name) | Deletes the specified database. If no database by that name
exists, no exception will be raised; instead, nothing at all
is done. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L446-L453 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.update_user | def update_user(self, user, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
return self._user_manager.update(user, name=name, password=password,
host=host) | python | def update_user(self, user, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
return self._user_manager.update(user, name=name, password=password,
host=host) | Allows you to change one or more of the user's username, password, or
host. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L466-L472 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.grant_user_access | def grant_user_access(self, user, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user.
"""
return self._user_manager.grant_user_access(user, db_names,
strict=strict) | python | def grant_user_access(self, user, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user.
"""
return self._user_manager.grant_user_access(user, db_names,
strict=strict) | Gives access to the databases listed in `db_names` to the user. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L483-L488 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.revoke_user_access | def revoke_user_access(self, user, db_names, strict=True):
"""
Revokes access to the databases listed in `db_names` for the user.
"""
return self._user_manager.revoke_user_access(user, db_names,
strict=strict) | python | def revoke_user_access(self, user, db_names, strict=True):
"""
Revokes access to the databases listed in `db_names` for the user.
"""
return self._user_manager.revoke_user_access(user, db_names,
strict=strict) | Revokes access to the databases listed in `db_names` for the user. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L491-L496 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.delete_user | def delete_user(self, user):
"""
Deletes the specified user. If no user by that name
exists, no exception will be raised; instead, nothing at all
is done.
"""
name = utils.get_name(user)
self._user_manager.delete(name) | python | def delete_user(self, user):
"""
Deletes the specified user. If no user by that name
exists, no exception will be raised; instead, nothing at all
is done.
"""
name = utils.get_name(user)
self._user_manager.delete(name) | Deletes the specified user. If no user by that name
exists, no exception will be raised; instead, nothing at all
is done. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L499-L506 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.enable_root_user | def enable_root_user(self):
"""
Enables login from any host for the root user and provides
the user with a generated root password.
"""
uri = "/instances/%s/root" % self.id
resp, body = self.manager.api.method_post(uri)
return body["user"]["password"] | python | def enable_root_user(self):
"""
Enables login from any host for the root user and provides
the user with a generated root password.
"""
uri = "/instances/%s/root" % self.id
resp, body = self.manager.api.method_post(uri)
return body["user"]["password"] | Enables login from any host for the root user and provides
the user with a generated root password. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L509-L516 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.root_user_status | def root_user_status(self):
"""
Returns True or False, depending on whether the root user
for this instance has been enabled.
"""
uri = "/instances/%s/root" % self.id
resp, body = self.manager.api.method_get(uri)
return body["rootEnabled"] | python | def root_user_status(self):
"""
Returns True or False, depending on whether the root user
for this instance has been enabled.
"""
uri = "/instances/%s/root" % self.id
resp, body = self.manager.api.method_get(uri)
return body["rootEnabled"] | Returns True or False, depending on whether the root user
for this instance has been enabled. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L519-L526 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.resize | def resize(self, flavor):
"""Set the size of this instance to a different flavor."""
# We need the flavorRef, not the flavor or size.
flavorRef = self.manager.api._get_flavor_ref(flavor)
body = {"flavorRef": flavorRef}
self.manager.action(self, "resize", body=body) | python | def resize(self, flavor):
"""Set the size of this instance to a different flavor."""
# We need the flavorRef, not the flavor or size.
flavorRef = self.manager.api._get_flavor_ref(flavor)
body = {"flavorRef": flavorRef}
self.manager.action(self, "resize", body=body) | Set the size of this instance to a different flavor. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L534-L539 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.resize_volume | def resize_volume(self, size):
"""Changes the size of the volume for this instance."""
curr_size = self.volume.size
if size <= curr_size:
raise exc.InvalidVolumeResize("The new volume size must be larger "
"than the current volume size of '%s'." % curr_size)
... | python | def resize_volume(self, size):
"""Changes the size of the volume for this instance."""
curr_size = self.volume.size
if size <= curr_size:
raise exc.InvalidVolumeResize("The new volume size must be larger "
"than the current volume size of '%s'." % curr_size)
... | Changes the size of the volume for this instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L542-L549 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.list_backups | def list_backups(self, limit=20, marker=0):
"""
Returns a paginated list of backups for this instance.
"""
return self.manager._list_backups_for_instance(self, limit=limit,
marker=marker) | python | def list_backups(self, limit=20, marker=0):
"""
Returns a paginated list of backups for this instance.
"""
return self.manager._list_backups_for_instance(self, limit=limit,
marker=marker) | Returns a paginated list of backups for this instance. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L552-L557 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseInstance.create_backup | def create_backup(self, name, description=None):
"""
Creates a backup of this instance, giving it the specified name along
with an optional description.
"""
return self.manager.create_backup(self, name, description=description) | python | def create_backup(self, name, description=None):
"""
Creates a backup of this instance, giving it the specified name along
with an optional description.
"""
return self.manager.create_backup(self, name, description=description) | Creates a backup of this instance, giving it the specified name along
with an optional description. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L560-L565 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUser.update | def update(self, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
return self.manager.update(self, name=name, password=password,
host=host) | python | def update(self, name=None, password=None, host=None):
"""
Allows you to change one or more of the user's username, password, or
host.
"""
return self.manager.update(self, name=name, password=password,
host=host) | Allows you to change one or more of the user's username, password, or
host. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L625-L631 |
pycontribs/pyrax | pyrax/clouddatabases.py | CloudDatabaseUser.grant_user_access | def grant_user_access(self, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user.
"""
return self.manager.grant_user_access(self, db_names, strict=strict) | python | def grant_user_access(self, db_names, strict=True):
"""
Gives access to the databases listed in `db_names` to the user.
"""
return self.manager.grant_user_access(self, db_names, strict=strict) | Gives access to the databases listed in `db_names` to the user. | https://github.com/pycontribs/pyrax/blob/9ddfd5064b3a292d7337906f3b2d5dce95b50b99/pyrax/clouddatabases.py#L642-L646 |
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