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openvax/isovar | isovar/variant_sequences.py | filter_variant_sequences | def filter_variant_sequences(
variant_sequences,
preferred_sequence_length,
min_variant_sequence_coverage=MIN_VARIANT_SEQUENCE_COVERAGE,):
"""
Drop variant sequences which are shorter than request or don't have
enough supporting reads.
"""
variant_sequences = trim_variant_seq... | python | def filter_variant_sequences(
variant_sequences,
preferred_sequence_length,
min_variant_sequence_coverage=MIN_VARIANT_SEQUENCE_COVERAGE,):
"""
Drop variant sequences which are shorter than request or don't have
enough supporting reads.
"""
variant_sequences = trim_variant_seq... | [
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openvax/isovar | isovar/variant_sequences.py | reads_generator_to_sequences_generator | def reads_generator_to_sequences_generator(
variant_and_reads_generator,
min_alt_rna_reads=MIN_ALT_RNA_READS,
min_variant_sequence_coverage=MIN_VARIANT_SEQUENCE_COVERAGE,
preferred_sequence_length=VARIANT_SEQUENCE_LENGTH,
variant_sequence_assembly=VARIANT_SEQUENCE_ASSEMBLY):
... | python | def reads_generator_to_sequences_generator(
variant_and_reads_generator,
min_alt_rna_reads=MIN_ALT_RNA_READS,
min_variant_sequence_coverage=MIN_VARIANT_SEQUENCE_COVERAGE,
preferred_sequence_length=VARIANT_SEQUENCE_LENGTH,
variant_sequence_assembly=VARIANT_SEQUENCE_ASSEMBLY):
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Parameters
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variant_and_reads_generator : generator
Sequence of Variant objects paired with a list of reads which
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min_alt_rna_reads :... | [
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.contains | def contains(self, other):
"""
Is the other VariantSequence a subsequence of this one?
The two sequences must agree on the alt nucleotides, the prefix of the
longer must contain the prefix of the shorter, and the suffix of the
longer must contain the suffix of the shorter.
... | python | def contains(self, other):
"""
Is the other VariantSequence a subsequence of this one?
The two sequences must agree on the alt nucleotides, the prefix of the
longer must contain the prefix of the shorter, and the suffix of the
longer must contain the suffix of the shorter.
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.left_overlaps | def left_overlaps(self, other, min_overlap_size=1):
"""
Does this VariantSequence overlap another on the left side?
"""
if self.alt != other.alt:
# allele must match!
return False
if len(other.prefix) > len(self.prefix):
# only consider strin... | python | def left_overlaps(self, other, min_overlap_size=1):
"""
Does this VariantSequence overlap another on the left side?
"""
if self.alt != other.alt:
# allele must match!
return False
if len(other.prefix) > len(self.prefix):
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.add_reads | def add_reads(self, reads):
"""
Create another VariantSequence with more supporting reads.
"""
if len(reads) == 0:
return self
new_reads = self.reads.union(reads)
if len(new_reads) > len(self.reads):
return VariantSequence(
prefix=s... | python | def add_reads(self, reads):
"""
Create another VariantSequence with more supporting reads.
"""
if len(reads) == 0:
return self
new_reads = self.reads.union(reads)
if len(new_reads) > len(self.reads):
return VariantSequence(
prefix=s... | [
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.variant_indices | def variant_indices(self):
"""
When we combine prefix + alt + suffix into a single string,
what are is base-0 index interval which gets us back the alt
sequence? First returned index is inclusive, the second is exclusive.
"""
variant_start_index = len(self.prefix)
... | python | def variant_indices(self):
"""
When we combine prefix + alt + suffix into a single string,
what are is base-0 index interval which gets us back the alt
sequence? First returned index is inclusive, the second is exclusive.
"""
variant_start_index = len(self.prefix)
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.coverage | def coverage(self):
"""
Returns NumPy array indicating number of reads covering each
nucleotides of this sequence.
"""
variant_start_index, variant_end_index = self.variant_indices()
n_nucleotides = len(self)
coverage_array = np.zeros(n_nucleotides, dtype="int32")... | python | def coverage(self):
"""
Returns NumPy array indicating number of reads covering each
nucleotides of this sequence.
"""
variant_start_index, variant_end_index = self.variant_indices()
n_nucleotides = len(self)
coverage_array = np.zeros(n_nucleotides, dtype="int32")... | [
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openvax/isovar | isovar/variant_sequences.py | VariantSequence.trim_by_coverage | def trim_by_coverage(self, min_reads):
"""
Given the min number of reads overlapping each nucleotide of
a variant sequence, trim this sequence by getting rid of positions
which are overlapped by fewer reads than specified.
"""
read_count_array = self.coverage()
lo... | python | def trim_by_coverage(self, min_reads):
"""
Given the min number of reads overlapping each nucleotide of
a variant sequence, trim this sequence by getting rid of positions
which are overlapped by fewer reads than specified.
"""
read_count_array = self.coverage()
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openvax/isovar | isovar/string_helpers.py | trim_N_nucleotides | def trim_N_nucleotides(prefix, suffix):
"""
Drop all occurrences of 'N' from prefix and suffix nucleotide strings
by trimming.
"""
if 'N' in prefix:
# trim prefix to exclude all occurrences of N
rightmost_index = prefix.rfind('N')
logger.debug(
"Trimming %d nucleo... | python | def trim_N_nucleotides(prefix, suffix):
"""
Drop all occurrences of 'N' from prefix and suffix nucleotide strings
by trimming.
"""
if 'N' in prefix:
# trim prefix to exclude all occurrences of N
rightmost_index = prefix.rfind('N')
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openvax/isovar | isovar/string_helpers.py | convert_from_bytes_if_necessary | def convert_from_bytes_if_necessary(prefix, suffix):
"""
Depending on how we extract data from pysam we may end up with either
a string or a byte array of nucleotides. For consistency and simplicity,
we want to only use strings in the rest of our code.
"""
if isinstance(prefix, bytes):
p... | python | def convert_from_bytes_if_necessary(prefix, suffix):
"""
Depending on how we extract data from pysam we may end up with either
a string or a byte array of nucleotides. For consistency and simplicity,
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"""
if isinstance(prefix, bytes):
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | Producer.publish | def publish(self, data, **kwargs):
"""Validate operation type."""
assert data.get('op') in {'index', 'create', 'delete', 'update'}
return super(Producer, self).publish(data, **kwargs) | python | def publish(self, data, **kwargs):
"""Validate operation type."""
assert data.get('op') in {'index', 'create', 'delete', 'update'}
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer.index | def index(self, record):
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer.process_bulk_queue | def process_bulk_queue(self, es_bulk_kwargs=None):
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"""
with current_celery_app.pool.acquire(block=True) as conn:
consumer = Consumer(
... | python | def process_bulk_queue(self, es_bulk_kwargs=None):
"""Process bulk indexing queue.
:param dict es_bulk_kwargs: Passed to
:func:`elasticsearch:elasticsearch.helpers.bulk`.
"""
with current_celery_app.pool.acquire(block=True) as conn:
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer._bulk_op | def _bulk_op(self, record_id_iterator, op_type, index=None, doc_type=None):
"""Index record in Elasticsearch asynchronously.
:param record_id_iterator: Iterator that yields record UUIDs.
:param op_type: Indexing operation (one of ``index``, ``create``,
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... | python | def _bulk_op(self, record_id_iterator, op_type, index=None, doc_type=None):
"""Index record in Elasticsearch asynchronously.
:param record_id_iterator: Iterator that yields record UUIDs.
:param op_type: Indexing operation (one of ``index``, ``create``,
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer._actionsiter | def _actionsiter(self, message_iterator):
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"""
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payload = message.decode()
try:
if payload['op'] == 'delete':
... | python | def _actionsiter(self, message_iterator):
"""Iterate bulk actions.
:param message_iterator: Iterator yielding messages from a queue.
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for message in message_iterator:
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer._delete_action | def _delete_action(self, payload):
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:returns: Dictionary defining an Elasticsearch bulk 'delete' action.
"""
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"""Bulk delete action.
:param payload: Decoded message body.
:returns: Dictionary defining an Elasticsearch bulk 'delete' action.
"""
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer._index_action | def _index_action(self, payload):
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"""
record = Record.get_record(payload['id'])
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"""Bulk index action.
:param payload: Decoded message body.
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"""
record = Record.get_record(payload['id'])
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inveniosoftware/invenio-indexer | invenio_indexer/api.py | RecordIndexer._prepare_record | def _prepare_record(record, index, doc_type):
"""Prepare record data for indexing.
:param record: The record to prepare.
:param index: The Elasticsearch index.
:param doc_type: The Elasticsearch document type.
:returns: The record metadata.
"""
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"""Prepare record data for indexing.
:param record: The record to prepare.
:param index: The Elasticsearch index.
:param doc_type: The Elasticsearch document type.
:returns: The record metadata.
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openvax/isovar | isovar/assembly.py | greedy_merge_helper | def greedy_merge_helper(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Returns a list of merged VariantSequence objects, and True if any
were successfully merged.
"""
merged_variant_sequences = {}
merged_any = False
# here we'll keep tr... | python | def greedy_merge_helper(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Returns a list of merged VariantSequence objects, and True if any
were successfully merged.
"""
merged_variant_sequences = {}
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openvax/isovar | isovar/assembly.py | greedy_merge | def greedy_merge(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Greedily merge overlapping sequences into longer sequences.
Accepts a collection of VariantSequence objects and returns another
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variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Greedily merge overlapping sequences into longer sequences.
Accepts a collection of VariantSequence objects and returns another
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openvax/isovar | isovar/assembly.py | collapse_substrings | def collapse_substrings(variant_sequences):
"""
Combine shorter sequences which are fully contained in longer sequences.
Parameters
----------
variant_sequences : list
List of VariantSequence objects
Returns a (potentially shorter) list without any contained subsequences.
"""
if... | python | def collapse_substrings(variant_sequences):
"""
Combine shorter sequences which are fully contained in longer sequences.
Parameters
----------
variant_sequences : list
List of VariantSequence objects
Returns a (potentially shorter) list without any contained subsequences.
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openvax/isovar | isovar/assembly.py | iterative_overlap_assembly | def iterative_overlap_assembly(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
Assembles longer sequences from reads centered on a variant by
between merging all pairs of overlapping sequences and collapsing
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variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
"""
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openvax/isovar | isovar/common.py | groupby | def groupby(xs, key_fn):
"""
Group elements of the list `xs` by keys generated from calling `key_fn`.
Returns a dictionary which maps keys to sub-lists of `xs`.
"""
result = defaultdict(list)
for x in xs:
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result[key].append(x)
return result | python | def groupby(xs, key_fn):
"""
Group elements of the list `xs` by keys generated from calling `key_fn`.
Returns a dictionary which maps keys to sub-lists of `xs`.
"""
result = defaultdict(list)
for x in xs:
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bskinn/opan | opan/utils/vector.py | ortho_basis | def ortho_basis(normal, ref_vec=None):
"""Generates an orthonormal basis in the plane perpendicular to `normal`
The orthonormal basis generated spans the plane defined with `normal` as
its normal vector. The handedness of `on1` and `on2` in the returned
basis is such that:
.. math::
... | python | def ortho_basis(normal, ref_vec=None):
"""Generates an orthonormal basis in the plane perpendicular to `normal`
The orthonormal basis generated spans the plane defined with `normal` as
its normal vector. The handedness of `on1` and `on2` in the returned
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.. math::
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bskinn/opan | opan/utils/vector.py | orthonorm_check | def orthonorm_check(a, tol=_DEF.ORTHONORM_TOL, report=False):
"""Checks orthonormality of the column vectors of a matrix.
If a one-dimensional |nparray| is passed to `a`, it is treated as a single
column vector, rather than a row matrix of length-one column vectors.
The matrix `a` does not need to be ... | python | def orthonorm_check(a, tol=_DEF.ORTHONORM_TOL, report=False):
"""Checks orthonormality of the column vectors of a matrix.
If a one-dimensional |nparray| is passed to `a`, it is treated as a single
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bskinn/opan | opan/utils/vector.py | parallel_check | def parallel_check(vec1, vec2):
"""Checks whether two vectors are parallel OR anti-parallel.
Vectors must be of the same dimension.
Parameters
----------
vec1
length-R |npfloat_| --
First vector to compare
vec2
length-R |npfloat_| --
Second vector to compare
... | python | def parallel_check(vec1, vec2):
"""Checks whether two vectors are parallel OR anti-parallel.
Vectors must be of the same dimension.
Parameters
----------
vec1
length-R |npfloat_| --
First vector to compare
vec2
length-R |npfloat_| --
Second vector to compare
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bskinn/opan | opan/utils/vector.py | proj | def proj(vec, vec_onto):
""" Vector projection.
Calculated as:
.. math::
\\mathsf{vec\\_onto} * \\frac{\\mathsf{vec}\\cdot\\mathsf{vec\\_onto}}
{\\mathsf{vec\\_onto}\\cdot\\mathsf{vec\\_onto}}
Parameters
----------
vec
length-R |npfloat_| --
Vector to projec... | python | def proj(vec, vec_onto):
""" Vector projection.
Calculated as:
.. math::
\\mathsf{vec\\_onto} * \\frac{\\mathsf{vec}\\cdot\\mathsf{vec\\_onto}}
{\\mathsf{vec\\_onto}\\cdot\\mathsf{vec\\_onto}}
Parameters
----------
vec
length-R |npfloat_| --
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bskinn/opan | opan/utils/vector.py | rej | def rej(vec, vec_onto):
""" Vector rejection.
Calculated by subtracting from `vec` the projection of `vec` onto
`vec_onto`:
.. math::
\\mathsf{vec} - \\mathrm{proj}\\left(\\mathsf{vec},
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Parameters
----------
vec
length-R |npfloat_| ... | python | def rej(vec, vec_onto):
""" Vector rejection.
Calculated by subtracting from `vec` the projection of `vec` onto
`vec_onto`:
.. math::
\\mathsf{vec} - \\mathrm{proj}\\left(\\mathsf{vec},
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Parameters
----------
vec
length-R |npfloat_| ... | [
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bskinn/opan | opan/utils/vector.py | vec_angle | def vec_angle(vec1, vec2):
""" Angle between two R-dimensional vectors.
Angle calculated as:
.. math::
\\arccos\\left[
\\frac{\\mathsf{vec1}\cdot\\mathsf{vec2}}
{\\left\\|\\mathsf{vec1}\\right\\|
\\left\\|\\mathsf{vec2}\\right\\|}
\\right]
Parameters
-... | python | def vec_angle(vec1, vec2):
""" Angle between two R-dimensional vectors.
Angle calculated as:
.. math::
\\arccos\\left[
\\frac{\\mathsf{vec1}\cdot\\mathsf{vec2}}
{\\left\\|\\mathsf{vec1}\\right\\|
\\left\\|\\mathsf{vec2}\\right\\|}
\\right]
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matthewwithanm/django-classbasedsettings | cbsettings/importers.py | new_module | def new_module(name):
"""
Do all of the gruntwork associated with creating a new module.
"""
parent = None
if '.' in name:
parent_name = name.rsplit('.', 1)[0]
parent = __import__(parent_name, fromlist=[''])
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openvax/isovar | isovar/allele_counts.py | allele_counts_dataframe | def allele_counts_dataframe(variant_and_allele_reads_generator):
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"""
df_builder = DataFrameBuilder(
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"""
Creates a DataFrame containing number of reads supporting the
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"""Install Postgres extension."""
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kmike/opencorpora-tools | opencorpora/reader.py | make_iterable | def make_iterable(obj, default=None):
""" Ensure obj is iterable. """
if obj is None:
return default or []
if isinstance(obj, (compat.string_types, compat.integer_types)):
return [obj]
return obj | python | def make_iterable(obj, default=None):
""" Ensure obj is iterable. """
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader.iter_documents | def iter_documents(self, fileids=None, categories=None, _destroy=False):
""" Return an iterator over corpus documents. """
doc_ids = self._filter_ids(fileids, categories)
for doc in imap(self.get_document, doc_ids):
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""" Return an iterator over corpus documents. """
doc_ids = self._filter_ids(fileids, categories)
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader._create_meta_cache | def _create_meta_cache(self):
""" Try to dump metadata to a file. """
try:
with open(self._cache_filename, 'wb') as f:
compat.pickle.dump(self._document_meta, f, 1)
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""" Try to dump metadata to a file. """
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader._load_meta_cache | def _load_meta_cache(self):
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader._compute_document_meta | def _compute_document_meta(self):
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Return documents meta information that can
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"""
meta = OrderedDict()
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Return documents meta information that can
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader._document_xml | def _document_xml(self, doc_id):
""" Return xml Element for the document document_id. """
doc_str = self._get_doc_by_raw_offset(str(doc_id))
return compat.ElementTree.XML(doc_str.encode('utf8')) | python | def _document_xml(self, doc_id):
""" Return xml Element for the document document_id. """
doc_str = self._get_doc_by_raw_offset(str(doc_id))
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kmike/opencorpora-tools | opencorpora/reader.py | CorpusReader._get_doc_by_line_offset | def _get_doc_by_line_offset(self, doc_id):
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bounds = self._get_meta()[str(doc_id)].bounds
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pyviz/imagen | imagen/colorspaces.py | _threeDdot_simple | def _threeDdot_simple(M,a):
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L = np.dot(M,A)
... | python | def _threeDdot_simple(M,a):
"Return Ma, where M is a 3x3 transformation matrix, for each pixel"
result = np.empty(a.shape,dtype=a.dtype)
for i in range(a.shape[0]):
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pyviz/imagen | imagen/colorspaces.py | _swaplch | def _swaplch(LCH):
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try: # Numpy array
L,C,H = np.dsplit(LCH,3)
return np.dstack((H,C,L))
except: # Tuple
L,C,H = LCH
return H,C,L | python | def _swaplch(LCH):
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pyviz/imagen | imagen/colorspaces.py | ColorSpace.rgb_to_hsv | def rgb_to_hsv(self,RGB):
"linear rgb to hsv"
gammaRGB = self._gamma_rgb(RGB)
return self._ABC_to_DEF_by_fn(gammaRGB,rgb_to_hsv) | python | def rgb_to_hsv(self,RGB):
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gammaRGB = self._gamma_rgb(RGB)
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pyviz/imagen | imagen/colorspaces.py | ColorSpace.hsv_to_rgb | def hsv_to_rgb(self,HSV):
"hsv to linear rgb"
gammaRGB = self._ABC_to_DEF_by_fn(HSV,hsv_to_rgb)
return self._ungamma_rgb(gammaRGB) | python | def hsv_to_rgb(self,HSV):
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pyviz/imagen | imagen/colorspaces.py | ColorConverter.image2working | def image2working(self,i):
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return self.colorspace.convert(self.image_space,
self.working_space, i) | python | def image2working(self,i):
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pyviz/imagen | imagen/image.py | edge_average | def edge_average(a):
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pyviz/imagen | imagen/image.py | FileImage._load_pil_image | def _load_pil_image(self, filename):
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inveniosoftware/invenio-indexer | invenio_indexer/cli.py | run | def run(delayed, concurrency, version_type=None, queue=None,
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inveniosoftware/invenio-indexer | invenio_indexer/cli.py | reindex | def reindex(pid_type):
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"""Reindex all records.
:param pid_type: Pid type.
"""
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inveniosoftware/invenio-indexer | invenio_indexer/cli.py | process_actions | def process_actions(actions):
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queue = current_app.config['INDEXER_MQ_QUEUE']
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q = queue(c)
for action in actions:
q = action(q) | python | def process_actions(actions):
"""Process queue actions."""
queue = current_app.config['INDEXER_MQ_QUEUE']
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def action(queue):
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return queue
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"""Initialize indexing queue."""
def action(queue):
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click.secho('Indexing queue has been initialized.', fg='green')
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inveniosoftware/invenio-indexer | invenio_indexer/cli.py | purge_queue | def purge_queue():
"""Purge indexing queue."""
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click.secho('Indexing queue has been purged.', fg='green')
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return action | python | def purge_queue():
"""Purge indexing queue."""
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inveniosoftware/invenio-indexer | invenio_indexer/cli.py | delete_queue | def delete_queue():
"""Delete indexing queue."""
def action(queue):
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click.secho('Indexing queue has been deleted.', fg='green')
return queue
return action | python | def delete_queue():
"""Delete indexing queue."""
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openvax/isovar | isovar/reference_sequence_key.py | variant_matches_reference_sequence | def variant_matches_reference_sequence(variant, ref_seq_on_transcript, strand):
"""
Make sure that reference nucleotides we expect to see on the reference
transcript from a variant are the same ones we encounter.
"""
if strand == "-":
ref_seq_on_transcript = reverse_complement_dna(ref_seq_on... | python | def variant_matches_reference_sequence(variant, ref_seq_on_transcript, strand):
"""
Make sure that reference nucleotides we expect to see on the reference
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happyleavesaoc/python-orvibo | orvibo/s20.py | _setup | def _setup():
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happyleavesaoc/python-orvibo | orvibo/s20.py | discover | def discover(timeout=DISCOVERY_TIMEOUT):
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hosts = {}
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""" Discover devices on the local network.
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"""
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"""
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""" Subscribe to the device.
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# Renew subscription if necessary
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happyleavesaoc/python-orvibo | orvibo/s20.py | S20._discovery_resp | def _discovery_resp(self, data):
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:param data: Payload.
:param addr: Address tuple.
:returns: MAC and reversed MAC.
"""
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... | python | def _discovery_resp(self, data):
""" Handle a discovery response.
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happyleavesaoc/python-orvibo | orvibo/s20.py | S20._subscribe_resp | def _subscribe_resp(self, data):
""" Handle a subscribe response.
:param data: Payload.
:returns: State (ON/OFF)
"""
if _is_subscribe_response(data):
status = bytes([data[23]])
_LOGGER.debug("Successfully subscribed to %s, state: %s",
... | python | def _subscribe_resp(self, data):
""" Handle a subscribe response.
:param data: Payload.
:returns: State (ON/OFF)
"""
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status = bytes([data[23]])
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happyleavesaoc/python-orvibo | orvibo/s20.py | S20._control_resp | def _control_resp(self, data, state):
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:returns: Acknowledged state.
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:returns: Acknowledged state.
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happyleavesaoc/python-orvibo | orvibo/s20.py | S20._udp_transact | def _udp_transact(self, payload, handler, *args,
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- Send payload multiple times.
- Wait for awhile to receive re... | python | def _udp_transact(self, payload, handler, *args,
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kmike/opencorpora-tools | opencorpora/reader_lxml.py | load | def load(source):
"""
Load OpenCorpora corpus.
The ``source`` can be any of the following:
- a file name/path
- a file object
- a file-like object
- a URL using the HTTP or FTP protocol
"""
parser = get_xml_parser()
return etree.parse(source, parser=parser).getroot() | python | def load(source):
"""
Load OpenCorpora corpus.
The ``source`` can be any of the following:
- a file name/path
- a file object
- a file-like object
- a URL using the HTTP or FTP protocol
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openvax/isovar | isovar/translation.py | translation_generator | def translation_generator(
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min_transcript_prefix_length,
max_transcript_mismatches,
include_mismatches_after_variant,
protein_sequence_length=None):
"""
Given all detected VariantSequence objects for a particular variant
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protein_sequence_length=None):
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openvax/isovar | isovar/translation.py | translate_variant_reads | def translate_variant_reads(
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openvax/isovar | isovar/translation.py | Translation.as_translation_key | def as_translation_key(self):
"""
Project Translation object or any other derived class into just a
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dictionary key.
"""
return TranslationKey(**{
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"""
Project Translation object or any other derived class into just a
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openvax/isovar | isovar/translation.py | Translation.from_variant_sequence_and_reference_context | def from_variant_sequence_and_reference_context(
cls,
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min_transcript_prefix_length,
max_transcript_mismatches,
include_mismatches_after_variant,
protein_sequence_length=None):
"""
Att... | python | def from_variant_sequence_and_reference_context(
cls,
variant_sequence,
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min_transcript_prefix_length,
max_transcript_mismatches,
include_mismatches_after_variant,
protein_sequence_length=None):
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imlonghao/cachet.python | cachet.py | Cachet.postComponents | def postComponents(self, name, status, **kwargs):
'''Create a new component.
:param name: Name of the component
:param status: Status of the component; 1-4
:param description: (optional) Description of the component
:param link: (optional) A hyperlink to the component
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'''Create a new component.
:param name: Name of the component
:param status: Status of the component; 1-4
:param description: (optional) Description of the component
:param link: (optional) A hyperlink to the component
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imlonghao/cachet.python | cachet.py | Cachet.postIncidents | def postIncidents(self, name, message, status, visible, **kwargs):
'''Create a new incident.
:param name: Name of the incident
:param message: A message (supporting Markdown) to explain more.
:param status: Status of the incident.
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imlonghao/cachet.python | cachet.py | Cachet.postMetrics | def postMetrics(self, name, suffix, description, default_value, **kwargs):
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:param description: Description of what the metric is measuring
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imlonghao/cachet.python | cachet.py | Cachet.postMetricsPointsByID | def postMetricsPointsByID(self, id, value, **kwargs):
'''Add a metric point to a given metric.
:param id: Metric ID
:param value: Value to plot on the metric graph
:param timestamp: Unix timestamp of the point was measured
:return: :class:`Response <Response>` object
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bskinn/opan | opan/utils/inertia.py | ctr_mass | def ctr_mass(geom, masses):
"""Calculate the center of mass of the indicated geometry.
Take a geometry and atom masses and compute the location of
the center of mass.
Parameters
----------
geom
length-3N |npfloat_| --
Coordinates of the atoms
masses
length-N OR len... | python | def ctr_mass(geom, masses):
"""Calculate the center of mass of the indicated geometry.
Take a geometry and atom masses and compute the location of
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Parameters
----------
geom
length-3N |npfloat_| --
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bskinn/opan | opan/utils/inertia.py | ctr_geom | 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
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""" Returns geometry shifted to center of mass.
Helper function to automate / encapsulate translation of a geometry to its
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geom
length-3N |npfloat_| --
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bskinn/opan | opan/utils/inertia.py | inertia_tensor | def inertia_tensor(geom, masses):
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provided geometry and atomic masses. Always recenters the
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Reference for inertia tensor: [Kro92]_, Eq. (2.26)
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"""Generate the 3x3 moment-of-inertia tensor.
Compute the 3x3 moment-of-inertia tensor for the
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"... | 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... | [
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] | 0b1b21662df6abc971407a9386db21a8796fbfe5 | https://github.com/bskinn/opan/blob/0b1b21662df6abc971407a9386db21a8796fbfe5/opan/utils/inertia.py#L164-L242 | train |
bskinn/opan | opan/utils/inertia.py | rot_consts | 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... | python | 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... | [
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Calculates the rotational constants for the provided system with numerical
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bskinn/opan | opan/utils/inertia.py | _fadn_orth | 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_| --
... | python | 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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Utility function to identify the first atomic displacement in a geometry
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bskinn/opan | opan/utils/inertia.py | _fadn_par | 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
... | python | 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
... | [
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Utility function to identify the first atomic displacement in a geometry
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Parameters
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length-3 |npfloat_| --
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openvax/isovar | isovar/reference_context.py | reference_contexts_for_variants | 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... | python | 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... | [
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Parameters
----------
variants : varcode.VariantCollection
context_size : int
Max of nucleotides to include to the left and right of the variant
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openvax/isovar | isovar/reference_context.py | variants_to_reference_contexts_dataframe | def variants_to_reference_contexts_dataframe(
variants,
context_size,
transcript_id_whitelist=None):
"""
Given a collection of variants, find all reference sequence contexts
around each variant.
Parameters
----------
variants : varcode.VariantCollection
context_size... | python | def variants_to_reference_contexts_dataframe(
variants,
context_size,
transcript_id_whitelist=None):
"""
Given a collection of variants, find all reference sequence contexts
around each variant.
Parameters
----------
variants : varcode.VariantCollection
context_size... | [
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Max of nucleotides to include to the left and right of the variant
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pyviz/imagen | imagen/patternfn.py | exponential | 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)) | python | 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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pyviz/imagen | imagen/patternfn.py | line | 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 =... | python | 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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pyviz/imagen | imagen/patternfn.py | disk | def disk(x, y, height, gaussian_width):
"""
Circular disk with Gaussian fall-off after the solid central region.
"""
disk_radius = height/2.0
distance_from_origin = np.sqrt(x**2+y**2)
distance_outside_disk = distance_from_origin - disk_radius
sigmasq = gaussian_width*gaussian_width
if ... | python | def disk(x, y, height, gaussian_width):
"""
Circular disk with Gaussian fall-off after the solid central region.
"""
disk_radius = height/2.0
distance_from_origin = np.sqrt(x**2+y**2)
distance_outside_disk = distance_from_origin - disk_radius
sigmasq = gaussian_width*gaussian_width
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