partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
train | ctr_geom | Returns geometry shifted to center of mass.
Helper function to automate / encapsulate translation of a geometry to its
center of mass.
Parameters
----------
geom
length-3N |npfloat_| --
Original coordinates of the atoms
masses
length-N OR length-3N |npfloat_| --
... | opan/utils/inertia.py | def ctr_geom(geom, masses):
""" Returns geometry shifted to center of mass.
Helper function to automate / encapsulate translation of a geometry to its
center of mass.
Parameters
----------
geom
length-3N |npfloat_| --
Original coordinates of the atoms
masses
length... | def ctr_geom(geom, masses):
""" Returns geometry shifted to center of mass.
Helper function to automate / encapsulate translation of a geometry to its
center of mass.
Parameters
----------
geom
length-3N |npfloat_| --
Original coordinates of the atoms
masses
length... | [
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train | inertia_tensor | Generate the 3x3 moment-of-inertia tensor.
Compute the 3x3 moment-of-inertia tensor for the
provided geometry and atomic masses. Always recenters the
geometry to the center of mass as the first step.
Reference for inertia tensor: [Kro92]_, Eq. (2.26)
.. todo:: Replace cite eventually with link t... | opan/utils/inertia.py | def inertia_tensor(geom, masses):
"""Generate the 3x3 moment-of-inertia tensor.
Compute the 3x3 moment-of-inertia tensor for the
provided geometry and atomic masses. Always recenters the
geometry to the center of mass as the first step.
Reference for inertia tensor: [Kro92]_, Eq. (2.26)
.. t... | def inertia_tensor(geom, masses):
"""Generate the 3x3 moment-of-inertia tensor.
Compute the 3x3 moment-of-inertia tensor for the
provided geometry and atomic masses. Always recenters the
geometry to the center of mass as the first step.
Reference for inertia tensor: [Kro92]_, Eq. (2.26)
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train | principals | Principal axes and moments of inertia for the indicated geometry.
Calculated by :func:`scipy.linalg.eigh`, since the moment of inertia tensor
is symmetric (real-Hermitian) by construction. More convenient to
compute both the axes and moments at the same time since the eigenvectors
must be processed to... | opan/utils/inertia.py | def principals(geom, masses, on_tol=_DEF.ORTHONORM_TOL):
"""Principal axes and moments of inertia for the indicated geometry.
Calculated by :func:`scipy.linalg.eigh`, since the moment of inertia tensor
is symmetric (real-Hermitian) by construction. More convenient to
compute both the axes and moments ... | def principals(geom, masses, on_tol=_DEF.ORTHONORM_TOL):
"""Principal axes and moments of inertia for the indicated geometry.
Calculated by :func:`scipy.linalg.eigh`, since the moment of inertia tensor
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train | rot_consts | Rotational constants for a given molecular system.
Calculates the rotational constants for the provided system with numerical
value given in the units provided in `units`. The orthnormality tolerance
`on_tol` is required in order to be passed through to the
:func:`principals` function.
If the sys... | opan/utils/inertia.py | def rot_consts(geom, masses, units=_EURC.INV_INERTIA, on_tol=_DEF.ORTHONORM_TOL):
"""Rotational constants for a given molecular system.
Calculates the rotational constants for the provided system with numerical
value given in the units provided in `units`. The orthnormality tolerance
`on_tol` is requi... | def rot_consts(geom, masses, units=_EURC.INV_INERTIA, on_tol=_DEF.ORTHONORM_TOL):
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Calculates the rotational constants for the provided system with numerical
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train | _fadn_orth | First non-zero Atomic Displacement Non-Orthogonal to Vec
Utility function to identify the first atomic displacement in a geometry
that is (a) not the zero vector; and (b) not normal to the reference vector.
Parameters
----------
vec
length-3 |npfloat_| --
Reference vector. Does not... | opan/utils/inertia.py | def _fadn_orth(vec, geom):
"""First non-zero Atomic Displacement Non-Orthogonal to Vec
Utility function to identify the first atomic displacement in a geometry
that is (a) not the zero vector; and (b) not normal to the reference vector.
Parameters
----------
vec
length-3 |npfloat_| --
... | def _fadn_orth(vec, geom):
"""First non-zero Atomic Displacement Non-Orthogonal to Vec
Utility function to identify the first atomic displacement in a geometry
that is (a) not the zero vector; and (b) not normal to the reference vector.
Parameters
----------
vec
length-3 |npfloat_| --
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train | _fadn_par | First non-zero Atomic Displacement that is Non-Parallel with Vec
Utility function to identify the first atomic displacement in a geometry
that is both (a) not the zero vector and (b) non-(anti-)parallel with a
reference vector.
Parameters
----------
vec
length-3 |npfloat_| --
R... | opan/utils/inertia.py | def _fadn_par(vec, geom):
"""First non-zero Atomic Displacement that is Non-Parallel with Vec
Utility function to identify the first atomic displacement in a geometry
that is both (a) not the zero vector and (b) non-(anti-)parallel with a
reference vector.
Parameters
----------
vec
... | def _fadn_par(vec, geom):
"""First non-zero Atomic Displacement that is Non-Parallel with Vec
Utility function to identify the first atomic displacement in a geometry
that is both (a) not the zero vector and (b) non-(anti-)parallel with a
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Parameters
----------
vec
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train | reference_contexts_for_variant | variant : varcode.Variant
context_size : int
Max of nucleotides to include to the left and right of the variant
in the context sequence.
transcript_id_whitelist : set, optional
If given, then only consider transcripts whose IDs are in this set.
Returns list of ReferenceContext obj... | isovar/reference_context.py | def reference_contexts_for_variant(
variant,
context_size,
transcript_id_whitelist=None):
"""
variant : varcode.Variant
context_size : int
Max of nucleotides to include to the left and right of the variant
in the context sequence.
transcript_id_whitelist : set, ... | def reference_contexts_for_variant(
variant,
context_size,
transcript_id_whitelist=None):
"""
variant : varcode.Variant
context_size : int
Max of nucleotides to include to the left and right of the variant
in the context sequence.
transcript_id_whitelist : set, ... | [
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train | reference_contexts_for_variants | Extract a set of reference contexts for each variant in the collection.
Parameters
----------
variants : varcode.VariantCollection
context_size : int
Max of nucleotides to include to the left and right of the variant
in the context sequence.
transcript_id_whitelist : set, optional... | isovar/reference_context.py | def reference_contexts_for_variants(
variants,
context_size,
transcript_id_whitelist=None):
"""
Extract a set of reference contexts for each variant in the collection.
Parameters
----------
variants : varcode.VariantCollection
context_size : int
Max of nucleotid... | def reference_contexts_for_variants(
variants,
context_size,
transcript_id_whitelist=None):
"""
Extract a set of reference contexts for each variant in the collection.
Parameters
----------
variants : varcode.VariantCollection
context_size : int
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train | variants_to_reference_contexts_dataframe | Given a collection of variants, find all reference sequence contexts
around each variant.
Parameters
----------
variants : varcode.VariantCollection
context_size : int
Max of nucleotides to include to the left and right of the variant
in the context sequence.
transcript_id_whi... | isovar/reference_context.py | def variants_to_reference_contexts_dataframe(
variants,
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transcript_id_whitelist=None):
"""
Given a collection of variants, find all reference sequence contexts
around each variant.
Parameters
----------
variants : varcode.VariantCollection
context_size... | def variants_to_reference_contexts_dataframe(
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Given a collection of variants, find all reference sequence contexts
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----------
variants : varcode.VariantCollection
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train | gaussian | Two-dimensional oriented Gaussian pattern (i.e., 2D version of a
bell curve, like a normal distribution but not necessarily summing
to 1.0). | imagen/patternfn.py | def gaussian(x, y, xsigma, ysigma):
"""
Two-dimensional oriented Gaussian pattern (i.e., 2D version of a
bell curve, like a normal distribution but not necessarily summing
to 1.0).
"""
if xsigma==0.0 or ysigma==0.0:
return x*0.0
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x_w = np.divide(x,x... | def gaussian(x, y, xsigma, ysigma):
"""
Two-dimensional oriented Gaussian pattern (i.e., 2D version of a
bell curve, like a normal distribution but not necessarily summing
to 1.0).
"""
if xsigma==0.0 or ysigma==0.0:
return x*0.0
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train | log_gaussian | Two-dimensional oriented Log Gaussian pattern (i.e., 2D version of a
bell curve with an independent, movable peak). Much like a normal
distribution, but not necessarily placing the peak above the center,
and not necessarily summing to 1.0). | imagen/patternfn.py | def log_gaussian(x, y, x_sigma, y_sigma, mu):
"""
Two-dimensional oriented Log Gaussian pattern (i.e., 2D version of a
bell curve with an independent, movable peak). Much like a normal
distribution, but not necessarily placing the peak above the center,
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"""
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"""
Two-dimensional oriented Log Gaussian pattern (i.e., 2D version of a
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train | exponential | Two-dimensional oriented exponential decay pattern. | imagen/patternfn.py | def exponential(x, y, xscale, yscale):
"""
Two-dimensional oriented exponential decay pattern.
"""
if xscale==0.0 or yscale==0.0:
return x*0.0
with float_error_ignore():
x_w = np.divide(x,xscale)
y_h = np.divide(y,yscale)
return np.exp(-np.sqrt(x_w*x_w+y_h*y_h)) | def exponential(x, y, xscale, yscale):
"""
Two-dimensional oriented exponential decay pattern.
"""
if xscale==0.0 or yscale==0.0:
return x*0.0
with float_error_ignore():
x_w = np.divide(x,xscale)
y_h = np.divide(y,yscale)
return np.exp(-np.sqrt(x_w*x_w+y_h*y_h)) | [
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train | gabor | Gabor pattern (sine grating multiplied by a circular Gaussian). | imagen/patternfn.py | def gabor(x, y, xsigma, ysigma, frequency, phase):
"""
Gabor pattern (sine grating multiplied by a circular Gaussian).
"""
if xsigma==0.0 or ysigma==0.0:
return x*0.0
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p = np.exp(-0.5*x_w*x... | def gabor(x, y, xsigma, ysigma, frequency, phase):
"""
Gabor pattern (sine grating multiplied by a circular Gaussian).
"""
if xsigma==0.0 or ysigma==0.0:
return x*0.0
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train | line | Infinite-length line with a solid central region, then Gaussian fall-off at the edges. | imagen/patternfn.py | def line(y, thickness, gaussian_width):
"""
Infinite-length line with a solid central region, then Gaussian fall-off at the edges.
"""
distance_from_line = abs(y)
gaussian_y_coord = distance_from_line - thickness/2.0
sigmasq = gaussian_width*gaussian_width
if sigmasq==0.0:
falloff =... | def line(y, thickness, gaussian_width):
"""
Infinite-length line with a solid central region, then Gaussian fall-off at the edges.
"""
distance_from_line = abs(y)
gaussian_y_coord = distance_from_line - thickness/2.0
sigmasq = gaussian_width*gaussian_width
if sigmasq==0.0:
falloff =... | [
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train | disk | Circular disk with Gaussian fall-off after the solid central region. | imagen/patternfn.py | def disk(x, y, height, gaussian_width):
"""
Circular disk with Gaussian fall-off after the solid central region.
"""
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distance_from_origin = np.sqrt(x**2+y**2)
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"""
Circular disk with Gaussian fall-off after the solid central region.
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train | ring | Circular ring (annulus) with Gaussian fall-off after the solid ring-shaped region. | imagen/patternfn.py | def ring(x, y, height, thickness, gaussian_width):
"""
Circular ring (annulus) with Gaussian fall-off after the solid ring-shaped region.
"""
radius = height/2.0
half_thickness = thickness/2.0
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Circular ring (annulus) with Gaussian fall-off after the solid ring-shaped region.
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train | smooth_rectangle | Rectangle with a solid central region, then Gaussian fall-off at the edges. | imagen/patternfn.py | def smooth_rectangle(x, y, rec_w, rec_h, gaussian_width_x, gaussian_width_y):
"""
Rectangle with a solid central region, then Gaussian fall-off at the edges.
"""
gaussian_x_coord = abs(x)-rec_w/2.0
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"""
Rectangle with a solid central region, then Gaussian fall-off at the edges.
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train | arc_by_radian | Radial arc with Gaussian fall-off after the solid ring-shaped
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"""
Radial arc with Gaussian fall-off after the solid ring-shaped
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"""
Radial arc with Gaussian fall-off after the solid ring-shaped
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train | arc_by_center | Arc with Gaussian fall-off after the solid ring-shaped region and specified
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This function calculates the start and end radian from the given width and
height, and then calls arc_by_radian function to draw the curve. | imagen/patternfn.py | def arc_by_center(x, y, arc_box, constant_length, thickness, gaussian_width):
"""
Arc with Gaussian fall-off after the solid ring-shaped region and specified
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train | skipPGVersionBefore | Skip PG versions below specific version i.e. (9, 5). | postpy/fixtures.py | def skipPGVersionBefore(*ver):
"""Skip PG versions below specific version i.e. (9, 5)."""
ver = ver + (0,) * (3 - len(ver))
def skip_before_postgres_(func):
@wraps(func)
def skip_before_postgres__(obj, *args, **kwargs):
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"""Pack an arbitrary set of iterables and non-iterables into tuples.
Function packs a set of inputs with arbitrary iterability into tuples.
Iterability is tested with :func:`iterable`. Non-iterable inputs
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train | template_subst | Perform substitution of content into tagged string.
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""" Perform substitution of content into tagged string.
For substitutions into template input files for external computational
packages, no checks for valid syntax are performed.
Each key in `subs` corresponds to a delimited
substitution tag t... | def template_subst(template, subs, delims=('<', '>')):
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train | tee_manager.advance | Advance the base iterator, publish to constituent iterators. | picklable_itertools/tee.py | def advance(self):
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train | SeparatedComposite.__distance_valid | Returns true if the distance between the (x,y) locations of
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"""
Returns true if the distance between the (x,y) locations of
two generators g0 and g1 is greater than a minimum separation.
Can be extended easily to support other criteria.
"""
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... | def __distance_valid(self, g0, g1, p):
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train | SuperOpanHess.check_geom | Check for consistency of Hessian geometry with input coords/atoms.
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train | OpanXYZ._load_data | Internal function for making XYZ object from explicit geom data.
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train | OpanXYZ.dist_iter | Iterator over selected interatomic distances.
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g... | def dist_iter(self, g_nums, ats_1, ats_2, invalid_error=False):
""" Iterator over selected interatomic distances.
Distances are in Bohrs as with :meth:`dist_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
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train | OpanXYZ.angle_single | Spanning angle among three atoms.
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Parameters
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... | opan/xyz.py | def angle_single(self, g_num, at_1, at_2, at_3):
""" Spanning angle among three atoms.
The indices `at_1` and `at_3` can be the same (yielding a
trivial zero angle), but `at_2` must be different from
both `at_1` and `at_3`.
Parameters
----------
g_num
... | def angle_single(self, g_num, at_1, at_2, at_3):
""" Spanning angle among three atoms.
The indices `at_1` and `at_3` can be the same (yielding a
trivial zero angle), but `at_2` must be different from
both `at_1` and `at_3`.
Parameters
----------
g_num
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train | OpanXYZ.angle_iter | Iterator over selected atomic angles.
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See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
g_nums
|int| or iterable |int| or |None| --
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""" Iterator over selected atomic angles.
Angles are in degrees as with :meth:`angle_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
g... | def angle_iter(self, g_nums, ats_1, ats_2, ats_3, invalid_error=False):
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Angles are in degrees as with :meth:`angle_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
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train | OpanXYZ.dihed_single | Dihedral/out-of-plane angle among four atoms.
Returns the out-of-plane angle among four atoms from geometry
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... | opan/xyz.py | def dihed_single(self, g_num, at_1, at_2, at_3, at_4):
""" Dihedral/out-of-plane angle among four atoms.
Returns the out-of-plane angle among four atoms from geometry
`g_num`, in degrees. The reference plane
is spanned by `at_1`, `at_2` and `at_3`. The out-of-plane angle is
def... | def dihed_single(self, g_num, at_1, at_2, at_3, at_4):
""" Dihedral/out-of-plane angle among four atoms.
Returns the out-of-plane angle among four atoms from geometry
`g_num`, in degrees. The reference plane
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train | OpanXYZ.dihed_iter | Iterator over selected dihedral angles.
Angles are in degrees as with :meth:`dihed_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
g_nums
|int| or iterable |int| or |None| --
Indices of the... | opan/xyz.py | def dihed_iter(self, g_nums, ats_1, ats_2, ats_3, ats_4, \
invalid_error=False):
""" Iterator over selected dihedral angles.
Angles are in degrees as with :meth:`dihed_single`.
See `above <toc-generators_>`_ for more information on
ca... | def dihed_iter(self, g_nums, ats_1, ats_2, ats_3, ats_4, \
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""" Iterator over selected dihedral angles.
Angles are in degrees as with :meth:`dihed_single`.
See `above <toc-generators_>`_ for more information on
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train | OpanXYZ.displ_single | Displacement vector between two atoms.
Returns the displacement vector pointing from `at_1`
toward `at_2` from geometry `g_num`.
If `at_1` == `at_2` a strict zero vector is returned.
Displacement vector is returned in units of Bohrs.
Parameters
----------
g_num... | opan/xyz.py | def displ_single(self, g_num, at_1, at_2):
""" Displacement vector between two atoms.
Returns the displacement vector pointing from `at_1`
toward `at_2` from geometry `g_num`.
If `at_1` == `at_2` a strict zero vector is returned.
Displacement vector is returned in units of Bohr... | def displ_single(self, g_num, at_1, at_2):
""" Displacement vector between two atoms.
Returns the displacement vector pointing from `at_1`
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train | OpanXYZ.displ_iter | Iterator over indicated displacement vectors.
Displacements are in Bohrs as with :meth:`displ_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
g_nums
|int| or length-R iterable |int| or |None| --
... | opan/xyz.py | def displ_iter(self, g_nums, ats_1, ats_2, invalid_error=False):
""" Iterator over indicated displacement vectors.
Displacements are in Bohrs as with :meth:`displ_single`.
See `above <toc-generators_>`_ for more information on
calling options.
Parameters
----------
... | def displ_iter(self, g_nums, ats_1, ats_2, invalid_error=False):
""" Iterator over indicated displacement vectors.
Displacements are in Bohrs as with :meth:`displ_single`.
See `above <toc-generators_>`_ for more information on
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Parameters
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train | OpanXYZ._none_subst | Helper function to insert full ranges for |None| for X_iter methods.
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""" Helper function to insert full ranges for |None| for X_iter methods.
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""" Helper function to insert full ranges for |None| for X_iter methods.
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train | OpanXYZ._iter_return | Wrapper for exception/|None| output handling of X_iter methods.
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Attempts to pass `tup` as arguments to `fxn`. If the call is
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... | def _iter_return(tup, fxn, invalid_error):
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train | guess_external_url | Return a URL that is most likely to route to `local_host` from outside.
The point is that we may be running on a remote host from the user's
point of view, so they can't access `local_host` from a Web browser just
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"... | def guess_external_url(local_host, port):
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train | DataFrameBuilder._check_column_lengths | Make sure columns are of the same length or else DataFrame construction
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"""
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"""
column_lengths_dict = {
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unique_column_length... | def _check_column_lengths(self):
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column_lengths_dict = {
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train | OpanVPT2.new_from_files | Initialize with data from files. | opan/vpt2/base.py | def new_from_files(self, basepath, basename, repo, \
bohrs=False, \
software=_E_SW.ORCA, \
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""" Initialize with data from files.
"""
# Imports
import os
from os import path as osp
... | def new_from_files(self, basepath, basename, repo, \
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software=_E_SW.ORCA, \
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""" Initialize with data from files.
"""
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import os
from os import path as osp
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train | literal_eval | Safely evaluate an expression node or a string containing a Python
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train | remote_exception | Metaclass that wraps exception type in RemoteException | mentor/utils.py | def remote_exception(exc, tb):
""" Metaclass that wraps exception type in RemoteException """
if type(exc) in exceptions:
typ = exceptions[type(exc)]
return typ(exc, tb)
else:
try:
typ = type(exc.__class__.__name__,
(RemoteException, type(exc)),
... | def remote_exception(exc, tb):
""" Metaclass that wraps exception type in RemoteException """
if type(exc) in exceptions:
typ = exceptions[type(exc)]
return typ(exc, tb)
else:
try:
typ = type(exc.__class__.__name__,
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train | allele_reads_from_locus_reads | Given a collection of LocusRead objects, returns a
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Parameters
----------
locus_reads : sequence of LocusRead records
n_ref : int
Number of reference nucleotides affected by variant.
Generate... | isovar/allele_reads.py | def allele_reads_from_locus_reads(locus_reads, n_ref):
"""
Given a collection of LocusRead objects, returns a
list of AlleleRead objects
(which are split into prefix/allele/suffix nucleotide strings).
Parameters
----------
locus_reads : sequence of LocusRead records
n_ref : int
... | def allele_reads_from_locus_reads(locus_reads, n_ref):
"""
Given a collection of LocusRead objects, returns a
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Parameters
----------
locus_reads : sequence of LocusRead records
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train | reads_overlapping_variant | Find reads in the given SAM/BAM file which overlap the given variant and
return them as a list of AlleleRead objects.
Parameters
----------
samfile : pysam.AlignmentFile
variant : varcode.Variant
chromosome : str
use_duplicate_reads : bool
Should we use reads that have been marke... | isovar/allele_reads.py | def reads_overlapping_variant(
samfile,
variant,
chromosome=None,
use_duplicate_reads=USE_DUPLICATE_READS,
use_secondary_alignments=USE_SECONDARY_ALIGNMENTS,
min_mapping_quality=MIN_READ_MAPPING_QUALITY):
"""
Find reads in the given SAM/BAM file which overlap the ... | def reads_overlapping_variant(
samfile,
variant,
chromosome=None,
use_duplicate_reads=USE_DUPLICATE_READS,
use_secondary_alignments=USE_SECONDARY_ALIGNMENTS,
min_mapping_quality=MIN_READ_MAPPING_QUALITY):
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train | reads_overlapping_variants | Generates sequence of tuples, each containing a variant paired with
a list of AlleleRead objects.
Parameters
----------
variants : varcode.VariantCollection
samfile : pysam.AlignmentFile
use_duplicate_reads : bool
Should we use reads that have been marked as PCR duplicates
use_se... | isovar/allele_reads.py | def reads_overlapping_variants(variants, samfile, **kwargs):
"""
Generates sequence of tuples, each containing a variant paired with
a list of AlleleRead objects.
Parameters
----------
variants : varcode.VariantCollection
samfile : pysam.AlignmentFile
use_duplicate_reads : bool
... | def reads_overlapping_variants(variants, samfile, **kwargs):
"""
Generates sequence of tuples, each containing a variant paired with
a list of AlleleRead objects.
Parameters
----------
variants : varcode.VariantCollection
samfile : pysam.AlignmentFile
use_duplicate_reads : bool
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train | group_reads_by_allele | Returns dictionary mapping each allele's nucleotide sequence to a list of
supporting AlleleRead objects. | isovar/allele_reads.py | def group_reads_by_allele(allele_reads):
"""
Returns dictionary mapping each allele's nucleotide sequence to a list of
supporting AlleleRead objects.
"""
allele_to_reads_dict = defaultdict(list)
for allele_read in allele_reads:
allele_to_reads_dict[allele_read.allele].append(allele_read)... | def group_reads_by_allele(allele_reads):
"""
Returns dictionary mapping each allele's nucleotide sequence to a list of
supporting AlleleRead objects.
"""
allele_to_reads_dict = defaultdict(list)
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train | reads_to_dataframe | Parameters
----------
variants_and_allele_reads : sequence
List or generator of pairs whose first element is a Variant and
whose second element is a sequence of AlleleRead objects. | isovar/allele_reads.py | def reads_to_dataframe(variants_and_allele_reads):
"""
Parameters
----------
variants_and_allele_reads : sequence
List or generator of pairs whose first element is a Variant and
whose second element is a sequence of AlleleRead objects.
"""
df_builder = DataFrameBuilder(
A... | def reads_to_dataframe(variants_and_allele_reads):
"""
Parameters
----------
variants_and_allele_reads : sequence
List or generator of pairs whose first element is a Variant and
whose second element is a sequence of AlleleRead objects.
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train | AlleleRead.from_locus_read | Given a single LocusRead object, return either an AlleleRead or None
Parameters
----------
locus_read : LocusRead
Read which overlaps a variant locus but doesn't necessarily contain the
alternate nucleotides
n_ref : int
Number of reference positions ... | isovar/allele_reads.py | def from_locus_read(cls, locus_read, n_ref):
"""
Given a single LocusRead object, return either an AlleleRead or None
Parameters
----------
locus_read : LocusRead
Read which overlaps a variant locus but doesn't necessarily contain the
alternate nucleotide... | def from_locus_read(cls, locus_read, n_ref):
"""
Given a single LocusRead object, return either an AlleleRead or None
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----------
locus_read : LocusRead
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train | nucleotide_counts | Count the number of times {A, C, T, G} occur at each position to the
left and right of the variant.
Parameters
----------
variant_reads : list of AlleleRead objects
Expected to all contain the same variant allele.
Returns a tuple with the following elements:
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"""
Count the number of times {A, C, T, G} occur at each position to the
left and right of the variant.
Parameters
----------
variant_reads : list of AlleleRead objects
Expected to all contain the same variant allele.
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"""
Count the number of times {A, C, T, G} occur at each position to the
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----------
variant_reads : list of AlleleRead objects
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train | most_common_nucleotides | Find the most common nucleotide at each offset to the left and
right of a variant.
Parameters
----------
partitioned_read_sequences : list of tuples
Each tuple has three elements:
- sequence before mutant nucleotides
- mutant nucleotides
- sequence after muta... | isovar/nucleotide_counts.py | def most_common_nucleotides(partitioned_read_sequences):
"""
Find the most common nucleotide at each offset to the left and
right of a variant.
Parameters
----------
partitioned_read_sequences : list of tuples
Each tuple has three elements:
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"""
Find the most common nucleotide at each offset to the left and
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Parameters
----------
partitioned_read_sequences : list of tuples
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train | point_displ | Calculate the displacement vector between two n-D points.
pt1 - pt2
.. todo:: Complete point_disp docstring | opan/utils/symm.py | def point_displ(pt1, pt2):
""" Calculate the displacement vector between two n-D points.
pt1 - pt2
.. todo:: Complete point_disp docstring
"""
#Imports
import numpy as np
# Make iterable
if not np.iterable(pt1):
pt1 = np.float64(np.array([pt1]))
else:
pt1 = np.fl... | def point_displ(pt1, pt2):
""" Calculate the displacement vector between two n-D points.
pt1 - pt2
.. todo:: Complete point_disp docstring
"""
#Imports
import numpy as np
# Make iterable
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.. todo:: Complete point_dist docstring
"""
# Imports
from scipy import linalg as spla
dist = spla.norm(point_displ(pt1, pt2))
return dist | def point_dist(pt1, pt2):
""" Calculate the Euclidean distance between two n-D points.
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.. todo:: Complete point_dist docstring
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# Imports
from scipy import linalg as spla
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a 90deg rotation of (1,0,0) around the z-axis (0,0,1) yields a point at
(0,1,0).
.. todo:: Complete ... | opan/utils/symm.py | def point_rotate(pt, ax, theta):
""" Rotate a 3-D point around a 3-D axis through the origin.
Handedness is a counter-clockwise rotation when viewing the rotation
axis as pointing at the observer. Thus, in a right-handed x-y-z frame,
a 90deg rotation of (1,0,0) around the z-axis (0,0,1) yields a point... | def point_rotate(pt, ax, theta):
""" Rotate a 3-D point around a 3-D axis through the origin.
Handedness is a counter-clockwise rotation when viewing the rotation
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nv defines the normal vector to the plane (needs not be normalized)
.. todo:: Complete point_reflect docstring
Raises
------
ValueError : If pt or nv are not reducible to 3-D vectors
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nv defines the normal vector to the plane (needs not be normalized)
.. todo:: Complete point_reflect docstring
Raises
------
ValueError : If pt or nv are not reducible to 3-D vectors
ValueError : I... | def point_reflect(pt, nv):
""" Reflect a 3-D point through a plane intersecting the origin.
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.. todo:: Complete point_reflect docstring
Raises
------
ValueError : If pt or nv are not reducible to 3-D vectors
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.. todo:: Complete geom_reflect docstring | opan/utils/symm.py | def geom_reflect(g, nv):
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g is assumed already translated to center of mass @ origin
.. todo:: Complete geom_reflect docstring
"""
# Imports
import numpy as np
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.. todo:: Complete geom_reflect docstring
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# Imports
import numpy as np
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Sense of rotation is the same as point_rotate
.. todo:: Complete geom_rotate docstring | opan/utils/symm.py | def geom_rotate(g, ax, theta):
""" Rotation symmetry operation.
ax is rotation axis
g is assumed already translated to center of mass @ origin
Sense of rotation is the same as point_rotate
.. todo:: Complete geom_rotate docstring
"""
# Imports
import numpy as np
# Force g to n-... | def geom_rotate(g, ax, theta):
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g is assumed already translated to center of mass @ origin
Sense of rotation is the same as point_rotate
.. todo:: Complete geom_rotate docstring
"""
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import numpy as np
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train | symm_op | Perform general point symmetry operation on a geometry.
.. todo:: Complete symm_op docstring | opan/utils/symm.py | def symm_op(g, ax, theta, do_refl):
""" Perform general point symmetry operation on a geometry.
.. todo:: Complete symm_op docstring
"""
# Imports
import numpy as np
# Depend on lower functions' geometry vector coercion. Just
# do the rotation and, if indicated, the reflection.
gx =... | def symm_op(g, ax, theta, do_refl):
""" Perform general point symmetry operation on a geometry.
.. todo:: Complete symm_op docstring
"""
# Imports
import numpy as np
# Depend on lower functions' geometry vector coercion. Just
# do the rotation and, if indicated, the reflection.
gx =... | [
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train | geom_symm_match | [Revised match factor calculation]
.. todo:: Complete geom_symm_match docstring | opan/utils/symm.py | def geom_symm_match(g, atwts, ax, theta, do_refl):
""" [Revised match factor calculation]
.. todo:: Complete geom_symm_match docstring
"""
# Imports
import numpy as np
from scipy import linalg as spla
# Convert g and atwts to n-D vectors
g = make_nd_vec(g, nd=None, t=np.float64, norm... | def geom_symm_match(g, atwts, ax, theta, do_refl):
""" [Revised match factor calculation]
.. todo:: Complete geom_symm_match docstring
"""
# Imports
import numpy as np
from scipy import linalg as spla
# Convert g and atwts to n-D vectors
g = make_nd_vec(g, nd=None, t=np.float64, norm... | [
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train | geom_find_rotsymm | Identify highest-order symmetry for a geometry on a given axis.
Regular and improper axes possible.
.. todo:: Complete geom_find_rotsymm docstring | opan/utils/symm.py | def geom_find_rotsymm(g, atwts, ax, improp, \
nmax=_DEF.SYMM_MATCH_NMAX, \
tol=_DEF.SYMM_MATCH_TOL):
""" Identify highest-order symmetry for a geometry on a given axis.
Regular and improper axes possible.
.. todo:: Complete geom_find_rotsymm docstring
"""
# Imports
import num... | def geom_find_rotsymm(g, atwts, ax, improp, \
nmax=_DEF.SYMM_MATCH_NMAX, \
tol=_DEF.SYMM_MATCH_TOL):
""" Identify highest-order symmetry for a geometry on a given axis.
Regular and improper axes possible.
.. todo:: Complete geom_find_rotsymm docstring
"""
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train | geom_check_axis | [Get max proper order and reflection for an axis]
.. todo:: Complete geom_parse_axis docstring | opan/utils/symm.py | def geom_check_axis(g, atwts, ax,
nmax=_DEF.SYMM_MATCH_NMAX,
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""" [Get max proper order and reflection for an axis]
.. todo:: Complete geom_parse_axis docstring
"""
# Imports
import numpy as np
# Store the max found rotation order of the geometry.
... | def geom_check_axis(g, atwts, ax,
nmax=_DEF.SYMM_MATCH_NMAX,
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""" [Get max proper order and reflection for an axis]
.. todo:: Complete geom_parse_axis docstring
"""
# Imports
import numpy as np
# Store the max found rotation order of the geometry.
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train | geom_find_group | [Find all(?) proper rotation axes (n > 1) and reflection planes.]
.. todo:: Complete geom_find_axes docstring INCLUDING NEW HEADER LINE
DEPENDS on principal axes and moments being sorted such that:
I_A <= I_B <= I_C
Logic flow developed using:
1) http://symmetry.otterbein.edu/common/image... | opan/utils/symm.py | def geom_find_group(g, atwts, pr_ax, mom, tt, \
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tol=_DEF.SYMM_MATCH_TOL, \
dig=_DEF.SYMM_ATWT_ROUND_DIGITS,
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.. todo:: Complete geom_find_axes docstring IN... | def geom_find_group(g, atwts, pr_ax, mom, tt, \
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dig=_DEF.SYMM_ATWT_ROUND_DIGITS,
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train | g_subset | Extract a subset of a geometry matching a desired atom.
.. todo:: Complete g_subset docstring | opan/utils/symm.py | def g_subset(g, atwts, atwt,
digits=_DEF.SYMM_ATWT_ROUND_DIGITS):
""" Extract a subset of a geometry matching a desired atom.
.. todo:: Complete g_subset docstring
"""
# Imports
import numpy as np
# Ensure g and atwts are n-D vectors
g = make_nd_vec(g, nd=None, t=np.float64, ... | def g_subset(g, atwts, atwt,
digits=_DEF.SYMM_ATWT_ROUND_DIGITS):
""" Extract a subset of a geometry matching a desired atom.
.. todo:: Complete g_subset docstring
"""
# Imports
import numpy as np
# Ensure g and atwts are n-D vectors
g = make_nd_vec(g, nd=None, t=np.float64, ... | [
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Ensure dimensionality 'n' if passed.
Cast to type 't' if passed
Normalize output if norm=True
.. todo:: Complete make_nd_vec docstring | opan/utils/symm.py | def make_nd_vec(v, nd=None, t=None, norm=False):
""" Coerce input to np.array() and validate dimensionality.
Ensure dimensionality 'n' if passed.
Cast to type 't' if passed
Normalize output if norm=True
.. todo:: Complete make_nd_vec docstring
"""
# Imports
import numpy as np
fro... | def make_nd_vec(v, nd=None, t=None, norm=False):
""" Coerce input to np.array() and validate dimensionality.
Ensure dimensionality 'n' if passed.
Cast to type 't' if passed
Normalize output if norm=True
.. todo:: Complete make_nd_vec docstring
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# Imports
import numpy as np
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train | mtx_refl | Generate block-diagonal reflection matrix about nv.
reps must be >=1 and indicates the number of times the reflection
matrix should be repeated along the block diagonal. Typically this
will be the number of atoms in a geometry.
.. todo:: Complete mtx_refl docstring | opan/utils/symm.py | def mtx_refl(nv, reps=1):
""" Generate block-diagonal reflection matrix about nv.
reps must be >=1 and indicates the number of times the reflection
matrix should be repeated along the block diagonal. Typically this
will be the number of atoms in a geometry.
.. todo:: Complete mtx_refl docstring
... | def mtx_refl(nv, reps=1):
""" Generate block-diagonal reflection matrix about nv.
reps must be >=1 and indicates the number of times the reflection
matrix should be repeated along the block diagonal. Typically this
will be the number of atoms in a geometry.
.. todo:: Complete mtx_refl docstring
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train | mtx_rot | Generate block-diagonal rotation matrix about ax.
[copy handedness from somewhere]
.. todo:: Complete mtx_rot docstring | opan/utils/symm.py | def mtx_rot(ax, theta, reps=1):
""" Generate block-diagonal rotation matrix about ax.
[copy handedness from somewhere]
.. todo:: Complete mtx_rot docstring
"""
# Imports
import numpy as np
from scipy import linalg as spla
from ..const import PRM
# Ensure |ax| is large enough for... | def mtx_rot(ax, theta, reps=1):
""" Generate block-diagonal rotation matrix about ax.
[copy handedness from somewhere]
.. todo:: Complete mtx_rot docstring
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import numpy as np
from scipy import linalg as spla
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train | ff | First-Fit
This is perhaps the simplest packing heuristic;
it simply packs items in the next available bin.
Complexity O(n^2) | mentor/binpack.py | def ff(items, targets):
"""First-Fit
This is perhaps the simplest packing heuristic;
it simply packs items in the next available bin.
Complexity O(n^2)
"""
bins = [(target, []) for target in targets]
skip = []
for item in items:
for target, content in bins:
if item... | def ff(items, targets):
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This is perhaps the simplest packing heuristic;
it simply packs items in the next available bin.
Complexity O(n^2)
"""
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skip = []
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train | mr | Max-Rest
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train | bf | Best-Fit
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train | bfd | Best-Fit Decreasing
Complexity O(n^2) | mentor/binpack.py | def bfd(items, targets, **kwargs):
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genom... | isovar/variant_sequence_in_reading_frame.py | def trim_sequences(variant_sequence, reference_context):
"""
A VariantSequence and ReferenceContext may contain a different number of
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always expressed in terms of the positive strand against which it aligned,
but reference tra... | def trim_sequences(variant_sequence, reference_context):
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train | count_mismatches_before_variant | Computes the number of mismatching nucleotides between two cDNA sequences before a variant
locus.
Parameters
----------
reference_prefix : str
cDNA sequence of a reference transcript before a variant locus
cdna_prefix : str
cDNA sequence detected from RNAseq before a variant locus | isovar/variant_sequence_in_reading_frame.py | def count_mismatches_before_variant(reference_prefix, cdna_prefix):
"""
Computes the number of mismatching nucleotides between two cDNA sequences before a variant
locus.
Parameters
----------
reference_prefix : str
cDNA sequence of a reference transcript before a variant locus
cdna... | def count_mismatches_before_variant(reference_prefix, cdna_prefix):
"""
Computes the number of mismatching nucleotides between two cDNA sequences before a variant
locus.
Parameters
----------
reference_prefix : str
cDNA sequence of a reference transcript before a variant locus
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train | count_mismatches_after_variant | Computes the number of mismatching nucleotides between two cDNA sequences after a variant locus.
Parameters
----------
reference_suffix : str
cDNA sequence of a reference transcript after a variant locus
cdna_suffix : str
cDNA sequence detected from RNAseq after a variant locus | isovar/variant_sequence_in_reading_frame.py | def count_mismatches_after_variant(reference_suffix, cdna_suffix):
"""
Computes the number of mismatching nucleotides between two cDNA sequences after a variant locus.
Parameters
----------
reference_suffix : str
cDNA sequence of a reference transcript after a variant locus
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"""
Computes the number of mismatching nucleotides between two cDNA sequences after a variant locus.
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----------
reference_suffix : str
cDNA sequence of a reference transcript after a variant locus
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train | compute_offset_to_first_complete_codon | Once we've aligned the variant sequence to the ReferenceContext, we need
to transfer reading frame from the reference transcripts to the variant
sequences.
Parameters
----------
offset_to_first_complete_reference_codon : int
n_trimmed_from_reference_sequence : int
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n_trimmed_from_reference_sequence):
"""
Once we've aligned the variant sequence to the ReferenceContext, we need
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P... | def compute_offset_to_first_complete_codon(
offset_to_first_complete_reference_codon,
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"""
Once we've aligned the variant sequence to the ReferenceContext, we need
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train | match_variant_sequence_to_reference_context | Iteratively trim low-coverage subsequences of a variant sequence
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are too few nucleotides left in the variant sequence.
Parameters
----------
variant_sequence : VariantSequence
Assembled sequence from RNA reads, will need to be to ... | isovar/variant_sequence_in_reading_frame.py | def match_variant_sequence_to_reference_context(
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max_transcript_mismatches,
include_mismatches_after_variant=False,
max_trimming_attempts=2):
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train | VariantSequenceInReadingFrame.from_variant_sequence_and_reference_context | Combines a VariantSequence with the reading frame implied by a
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offset to the first complete codon in the cDNA sequence.
Parameters
----------
variant_sequence : VariantSequence
reference_context : Refer... | isovar/variant_sequence_in_reading_frame.py | def from_variant_sequence_and_reference_context(
cls, variant_sequence, reference_context):
"""
Combines a VariantSequence with the reading frame implied by a
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train | translate_cdna | Given a cDNA sequence which is aligned to a reading frame, returns
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Parameters
----------
cdna_sequence : str
cDNA sequence which is expected to st... | isovar/genetic_code.py | def translate_cdna(
cdna_sequence,
first_codon_is_start=False,
mitochondrial=False):
"""
Given a cDNA sequence which is aligned to a reading frame, returns
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first_codon_is_start=False,
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train | GeneticCode._check_codons | If codon table is missing stop codons, then add them. | isovar/genetic_code.py | def _check_codons(self):
"""
If codon table is missing stop codons, then add them.
"""
for stop_codon in self.stop_codons:
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the translated sequence ended on a stop codon (or just ran out of codons).
Parameters
----------
cdna_sequence : str
cDNA sequence... | isovar/genetic_code.py | def translate(self, cdna_sequence, first_codon_is_start=False):
"""
Given a cDNA sequence which is aligned to a reading frame, returns
the translated protein sequence and a boolean flag indicating whether
the translated sequence ended on a stop codon (or just ran out of codons).
... | def translate(self, cdna_sequence, first_codon_is_start=False):
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Given a cDNA sequence which is aligned to a reading frame, returns
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the translated sequence ended on a stop codon (or just ran out of codons).
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train | GeneticCode.copy | Make copy of this GeneticCode object with optional replacement
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name,
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stop_codons=None,
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train | OrcaEngrad._load | Initialize :class:`OrcaEngrad` object from .engrad file
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----------
path
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train | Listener.start | Start listening to changes | raildriver/events.py | def start(self):
"""
Start listening to changes
"""
self.running = True
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Subscribe to given fields.
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Subscribe to given fields.
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* fuel level
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train | PatternGenerator.channels | Channels() adds a shared interface for single channel and
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] | pyviz/imagen | python | https://github.com/pyviz/imagen/blob/53c5685c880f54b42795964d8db50b02e8590e88/imagen/patterngenerator.py#L213-L228 | [
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... | 53c5685c880f54b42795964d8db50b02e8590e88 |
train | PatternGenerator._create_and_rotate_coordinate_arrays | Create pattern matrices from x and y vectors, and rotate them
to the specified orientation. | imagen/patterngenerator.py | def _create_and_rotate_coordinate_arrays(self, x, y, orientation):
"""
Create pattern matrices from x and y vectors, and rotate them
to the specified orientation.
"""
# Using this two-liner requires that x increase from left to
# right and y decrease from left to right; I... | def _create_and_rotate_coordinate_arrays(self, x, y, orientation):
"""
Create pattern matrices from x and y vectors, and rotate them
to the specified orientation.
"""
# Using this two-liner requires that x increase from left to
# right and y decrease from left to right; I... | [
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] | pyviz/imagen | python | https://github.com/pyviz/imagen/blob/53c5685c880f54b42795964d8db50b02e8590e88/imagen/patterngenerator.py#L246-L257 | [
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