code stringlengths 66 870k | docstring stringlengths 19 26.7k | func_name stringlengths 1 138 | language stringclasses 1
value | repo stringlengths 7 68 | path stringlengths 5 324 | url stringlengths 46 389 | license stringclasses 7
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def forward(self, x: Tensor, include_embeddings: bool = False):
"""
x : torch.Tensor, shape = (batch_size, n_mels, n_ctx)
the mel spectrogram of the audio
include_embeddings: bool
whether to include intermediate steps in the output
"""
x = F.gelu(self.conv... |
x : torch.Tensor, shape = (batch_size, n_mels, n_ctx)
the mel spectrogram of the audio
include_embeddings: bool
whether to include intermediate steps in the output
| forward | python | bytedance/LatentSync | latentsync/whisper/whisper/model.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/model.py | Apache-2.0 |
def forward(self, x: Tensor, xa: Tensor, kv_cache: Optional[dict] = None, include_embeddings: bool = False):
"""
x : torch.LongTensor, shape = (batch_size, <= n_ctx)
the text tokens
xa : torch.Tensor, shape = (batch_size, n_mels, n_audio_ctx)
the encoded audio features to... |
x : torch.LongTensor, shape = (batch_size, <= n_ctx)
the text tokens
xa : torch.Tensor, shape = (batch_size, n_mels, n_audio_ctx)
the encoded audio features to be attended on
include_embeddings : bool
Whether to include intermediate values in the output to th... | forward | python | bytedance/LatentSync | latentsync/whisper/whisper/model.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/model.py | Apache-2.0 |
def install_kv_cache_hooks(self, cache: Optional[dict] = None):
"""
The `MultiHeadAttention` module optionally accepts `kv_cache` which stores the key and value
tensors calculated for the previous positions. This method returns a dictionary that stores
all caches, and the necessary hooks... |
The `MultiHeadAttention` module optionally accepts `kv_cache` which stores the key and value
tensors calculated for the previous positions. This method returns a dictionary that stores
all caches, and the necessary hooks for the key and value projection modules that save the
intermediat... | install_kv_cache_hooks | python | bytedance/LatentSync | latentsync/whisper/whisper/model.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/model.py | Apache-2.0 |
def decode_with_timestamps(self, tokens) -> str:
"""
Timestamp tokens are above the special tokens' id range and are ignored by `decode()`.
This method decodes given tokens with timestamps tokens annotated, e.g. "<|1.08|>".
"""
outputs = [[]]
for token in tokens:
... |
Timestamp tokens are above the special tokens' id range and are ignored by `decode()`.
This method decodes given tokens with timestamps tokens annotated, e.g. "<|1.08|>".
| decode_with_timestamps | python | bytedance/LatentSync | latentsync/whisper/whisper/tokenizer.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/tokenizer.py | Apache-2.0 |
def language_token(self) -> int:
"""Returns the token id corresponding to the value of the `language` field"""
if self.language is None:
raise ValueError(f"This tokenizer does not have language token configured")
additional_tokens = dict(
zip(
self.tokeni... | Returns the token id corresponding to the value of the `language` field | language_token | python | bytedance/LatentSync | latentsync/whisper/whisper/tokenizer.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/tokenizer.py | Apache-2.0 |
def write_srt(transcript: Iterator[dict], file: TextIO):
"""
Write a transcript to a file in SRT format.
Example usage:
from pathlib import Path
from whisper.utils import write_srt
result = transcribe(model, audio_path, temperature=temperature, **args)
# save SRT
a... |
Write a transcript to a file in SRT format.
Example usage:
from pathlib import Path
from whisper.utils import write_srt
result = transcribe(model, audio_path, temperature=temperature, **args)
# save SRT
audio_basename = Path(audio_path).stem
with open(Path(out... | write_srt | python | bytedance/LatentSync | latentsync/whisper/whisper/utils.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/utils.py | Apache-2.0 |
def load_model(
name: str, device: Optional[Union[str, torch.device]] = None, download_root: str = None, in_memory: bool = False
) -> Whisper:
"""
Load a Whisper ASR model
Parameters
----------
name : str
one of the official model names listed by `whisper.available_models()`, or
... |
Load a Whisper ASR model
Parameters
----------
name : str
one of the official model names listed by `whisper.available_models()`, or
path to a model checkpoint containing the model dimensions and the model state_dict.
device : Union[str, torch.device]
the PyTorch device to ... | load_model | python | bytedance/LatentSync | latentsync/whisper/whisper/__init__.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/__init__.py | Apache-2.0 |
def remove_symbols_and_diacritics(s: str, keep=""):
"""
Replace any other markers, symbols, and punctuations with a space,
and drop any diacritics (category 'Mn' and some manual mappings)
"""
return "".join(
c
if c in keep
else ADDITIONAL_DIACRITICS[c]
if c in ADDITIO... |
Replace any other markers, symbols, and punctuations with a space,
and drop any diacritics (category 'Mn' and some manual mappings)
| remove_symbols_and_diacritics | python | bytedance/LatentSync | latentsync/whisper/whisper/normalizers/basic.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/normalizers/basic.py | Apache-2.0 |
def remove_symbols(s: str):
"""
Replace any other markers, symbols, punctuations with a space, keeping diacritics
"""
return "".join(
" " if unicodedata.category(c)[0] in "MSP" else c for c in unicodedata.normalize("NFKC", s)
) |
Replace any other markers, symbols, punctuations with a space, keeping diacritics
| remove_symbols | python | bytedance/LatentSync | latentsync/whisper/whisper/normalizers/basic.py | https://github.com/bytedance/LatentSync/blob/master/latentsync/whisper/whisper/normalizers/basic.py | Apache-2.0 |
def cpg():
"""
>>> # +--------------+-----------+-----------+-----------+
>>> # | Chromosome | Start | End | CpG |
>>> # | (category) | (int64) | (int64) | (int64) |
>>> # |--------------+-----------+-----------+-----------|
>>> # | chrX | 64181 | 64793 ... |
>>> # +--------------+-----------+-----------+-----------+
>>> # | Chromosome | Start | End | CpG |
>>> # | (category) | (int64) | (int64) | (int64) |
>>> # |--------------+-----------+-----------+-----------|
>>> # | chrX | 64181 | 64793 | 62 |
... | cpg | python | pyranges/pyranges | pyranges/data.py | https://github.com/pyranges/pyranges/blob/master/pyranges/data.py | MIT |
def ucsc_bed():
"""
>>> # +--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------+
>>> # | Chromosome | Start | End | Feature | gene_id | transcript_id | Strand | exon_number | transcript_name |
... |
>>> # +--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------+
>>> # | Chromosome | Start | End | Feature | gene_id | transcript_id | Strand | exon_number | transcript_name |
>>> # | (category) | ... | ucsc_bed | python | pyranges/pyranges | pyranges/data.py | https://github.com/pyranges/pyranges/blob/master/pyranges/data.py | MIT |
def tss(self):
"""Return the transcription start sites.
Returns the 5' for every interval with feature "transcript".
See Also
--------
pyranges.genomicfeatures.GenomicFeaturesMethods.tes : return the transcription end sites
Examples
--------
>>> gr = p... | Return the transcription start sites.
Returns the 5' for every interval with feature "transcript".
See Also
--------
pyranges.genomicfeatures.GenomicFeaturesMethods.tes : return the transcription end sites
Examples
--------
>>> gr = pr.data.ensembl_gtf()[["Sou... | tss | python | pyranges/pyranges | pyranges/genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/pyranges/genomicfeatures.py | MIT |
def tes(self, slack=0):
"""Return the transcription end sites.
Returns the 3' for every interval with feature "transcript".
See Also
--------
pyranges.genomicfeatures.GenomicFeaturesMethods.tss : return the transcription start sites
Examples
--------
>... | Return the transcription end sites.
Returns the 3' for every interval with feature "transcript".
See Also
--------
pyranges.genomicfeatures.GenomicFeaturesMethods.tss : return the transcription start sites
Examples
--------
>>> gr = pr.data.ensembl_gtf()[["Sou... | tes | python | pyranges/pyranges | pyranges/genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/pyranges/genomicfeatures.py | MIT |
def introns(self, by="gene", nb_cpu=1):
"""Return the introns.
Parameters
----------
by : str, {"gene", "transcript"}, default "gene"
Whether to find introns per gene or transcript.
nb_cpu: int, default 1
How many cpus to use. Can at most use 1 per chro... | Return the introns.
Parameters
----------
by : str, {"gene", "transcript"}, default "gene"
Whether to find introns per gene or transcript.
nb_cpu: int, default 1
How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple.
Will... | introns | python | pyranges/pyranges | pyranges/genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/pyranges/genomicfeatures.py | MIT |
def genome_bounds(gr, chromsizes, clip=False, only_right=False):
"""Remove or clip intervals outside of genome bounds.
Parameters
----------
gr : PyRanges
Input intervals
chromsizes : dict or PyRanges or pyfaidx.Fasta
Dict or PyRanges describing the lengths of the chromosomes.
... | Remove or clip intervals outside of genome bounds.
Parameters
----------
gr : PyRanges
Input intervals
chromsizes : dict or PyRanges or pyfaidx.Fasta
Dict or PyRanges describing the lengths of the chromosomes.
pyfaidx.Fasta object is also accepted since it conveniently loads... | genome_bounds | python | pyranges/pyranges | pyranges/genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/pyranges/genomicfeatures.py | MIT |
def tile_genome(genome, tile_size, tile_last=False):
"""Create a tiled genome.
Parameters
----------
chromsizes : dict or PyRanges
Dict or PyRanges describing the lengths of the chromosomes.
tile_size : int
Length of the tiles.
tile_last : bool, default False
Use gen... | Create a tiled genome.
Parameters
----------
chromsizes : dict or PyRanges
Dict or PyRanges describing the lengths of the chromosomes.
tile_size : int
Length of the tiles.
tile_last : bool, default False
Use genome length as end of last tile.
See Also
--------
... | tile_genome | python | pyranges/pyranges | pyranges/genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/pyranges/genomicfeatures.py | MIT |
def get_sequence(gr, path=None, pyfaidx_fasta=None):
"""Get the sequence of the intervals from a fasta file
Parameters
----------
gr : PyRanges
Coordinates.
path : str
Path to fasta file. It will be indexed using pyfaidx if an index is not found
pyfaidx_fasta : pyfaidx.Fasta... | Get the sequence of the intervals from a fasta file
Parameters
----------
gr : PyRanges
Coordinates.
path : str
Path to fasta file. It will be indexed using pyfaidx if an index is not found
pyfaidx_fasta : pyfaidx.Fasta
Alternative method to provide fasta target, as a p... | get_sequence | python | pyranges/pyranges | pyranges/get_fasta.py | https://github.com/pyranges/pyranges/blob/master/pyranges/get_fasta.py | MIT |
def get_transcript_sequence(gr, group_by, path=None, pyfaidx_fasta=None):
"""Get the sequence of mRNAs, e.g. joining intervals corresponding to exons of the same transcript
Parameters
----------
gr : PyRanges
Coordinates.
group_by : str or list of str
intervals are grouped by thi... | Get the sequence of mRNAs, e.g. joining intervals corresponding to exons of the same transcript
Parameters
----------
gr : PyRanges
Coordinates.
group_by : str or list of str
intervals are grouped by this/these ID column(s): these are exons belonging to same transcript
path : st... | get_transcript_sequence | python | pyranges/pyranges | pyranges/get_fasta.py | https://github.com/pyranges/pyranges/blob/master/pyranges/get_fasta.py | MIT |
def count_overlaps(grs, features=None, strandedness=None, how=None, nb_cpu=1):
"""Count overlaps in multiple pyranges.
Parameters
----------
grs : dict of PyRanges
The PyRanges to use as queries.
features : PyRanges, default None
The PyRanges to use as subject in the query. If No... | Count overlaps in multiple pyranges.
Parameters
----------
grs : dict of PyRanges
The PyRanges to use as queries.
features : PyRanges, default None
The PyRanges to use as subject in the query. If None, the PyRanges themselves are used as a query.
strandedness : {None, "same", "o... | count_overlaps | python | pyranges/pyranges | pyranges/multioverlap.py | https://github.com/pyranges/pyranges/blob/master/pyranges/multioverlap.py | MIT |
def fill_kwargs(kwargs):
"""Give the kwargs dict default options."""
defaults = {
"strandedness": None,
"overlap": True,
"how": None,
"invert": None,
"new_pos": None,
"suffixes": ["_a", "_b"],
"suffix": "_b",
"sparse": {"self": False, "other": Fal... | Give the kwargs dict default options. | fill_kwargs | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def __array_ufunc__(self, *args, **kwargs):
"""Apply unary numpy-function.
Apply function to all columns which are not index, i.e. Chromosome,
Start, End nor Strand.
Notes
-----
Function must produce a vector of equal length.
Examples
--------
... | Apply unary numpy-function.
Apply function to all columns which are not index, i.e. Chromosome,
Start, End nor Strand.
Notes
-----
Function must produce a vector of equal length.
Examples
--------
>>> gr = pr.from_dict({"Chromosome": [1, 2, 3], "Star... | __array_ufunc__ | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def __getattr__(self, name):
"""Return column.
Parameters
----------
name : str
Column to return
Returns
-------
pandas.Series
Example
-------
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100, 250], "End": [... | Return column.
Parameters
----------
name : str
Column to return
Returns
-------
pandas.Series
Example
-------
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100, 250], "End": [10, 125, 251]})
>>> gr.Start
... | __getattr__ | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def __setattr__(self, column_name, column):
"""Insert or update column.
Parameters
----------
column_name : str
Name of column to update or insert.
column : list, np.array or pd.Series
Data to insert.
Example
-------
>>> gr = ... | Insert or update column.
Parameters
----------
column_name : str
Name of column to update or insert.
column : list, np.array or pd.Series
Data to insert.
Example
-------
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100... | __setattr__ | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def __getitem__(self, val):
"""Fetch columns or subset on position.
If a list is provided, the column(s) in the list is returned. This subsets on columns.
If a numpy array is provided, it must be of type bool and the same length as the PyRanges.
Otherwise, a subset of the rows is retu... | Fetch columns or subset on position.
If a list is provided, the column(s) in the list is returned. This subsets on columns.
If a numpy array is provided, it must be of type bool and the same length as the PyRanges.
Otherwise, a subset of the rows is returned with the location info provided.
... | __getitem__ | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def apply(self, f, strand=None, as_pyranges=True, nb_cpu=1, **kwargs):
"""Apply a function to the PyRanges.
Parameters
----------
f : function
Function to apply on each DataFrame in a PyRanges
strand : bool, default None, i.e. auto
Whether to do operati... | Apply a function to the PyRanges.
Parameters
----------
f : function
Function to apply on each DataFrame in a PyRanges
strand : bool, default None, i.e. auto
Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use
chrom... | apply | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def apply_chunks(self, f, as_pyranges=False, nb_cpu=1, **kwargs):
"""Apply a row-based function to arbitrary partitions of the PyRanges.
apply_chunks speeds up the application of functions where the result is not affected by
applying the function to ordered, non-overlapping splits of the data.
... | Apply a row-based function to arbitrary partitions of the PyRanges.
apply_chunks speeds up the application of functions where the result is not affected by
applying the function to ordered, non-overlapping splits of the data.
Parameters
----------
f : function
Row-b... | apply_chunks | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def apply_pair(self, other, f, strandedness=None, as_pyranges=True, **kwargs):
"""Apply a function to a pair of PyRanges.
The function is applied to each chromosome or chromosome/strand pair found in at least one
of the PyRanges.
Parameters
----------
f : function
... | Apply a function to a pair of PyRanges.
The function is applied to each chromosome or chromosome/strand pair found in at least one
of the PyRanges.
Parameters
----------
f : function
Row-based or associative function to apply on the DataFrames.
strandedness... | apply_pair | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def as_df(self):
"""Return PyRanges as DataFrame.
Returns
-------
DataFrame
A DataFrame natural sorted on Chromosome and Strand. The ordering of rows within
chromosomes and strands is preserved.
See also
--------
PyRanges.df : Return Py... | Return PyRanges as DataFrame.
Returns
-------
DataFrame
A DataFrame natural sorted on Chromosome and Strand. The ordering of rows within
chromosomes and strands is preserved.
See also
--------
PyRanges.df : Return PyRanges as DataFrame.
... | as_df | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def assign(self, col, f, strand=None, nb_cpu=1, **kwargs):
"""Add or replace a column.
Does not change the original PyRanges.
Parameters
----------
col : str
Name of column.
f : function
Function to create new column.
strand : bool, d... | Add or replace a column.
Does not change the original PyRanges.
Parameters
----------
col : str
Name of column.
f : function
Function to create new column.
strand : bool, default None, i.e. auto
Whether to do operations on chromo... | assign | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def boundaries(self, group_by, agg=None):
"""Return the boundaries of groups of intervals (e.g. transcripts)
Parameters
----------
group_by : str or list of str
Name(s) of column(s) to group intervals
agg : dict or None
Defines how to aggregate metada... | Return the boundaries of groups of intervals (e.g. transcripts)
Parameters
----------
group_by : str or list of str
Name(s) of column(s) to group intervals
agg : dict or None
Defines how to aggregate metadata columns. Provided as
dictionary of col... | boundaries | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def calculate_frame(self, by):
"""Calculate the frame of each genomic interval, assuming all are coding sequences (CDS), and add it as column inplace.
After this, the input Pyranges will contain an added "Frame" column, which determines the base of the CDS that is the first base of a codon.
Res... | Calculate the frame of each genomic interval, assuming all are coding sequences (CDS), and add it as column inplace.
After this, the input Pyranges will contain an added "Frame" column, which determines the base of the CDS that is the first base of a codon.
Resulting values are in range between 0 and 2... | calculate_frame | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def cluster(self, strand=None, by=None, slack=0, count=False, nb_cpu=1):
"""Give overlapping intervals a common id.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to ignore strand information if PyRanges is stranded.
by : str or list, default ... | Give overlapping intervals a common id.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to ignore strand information if PyRanges is stranded.
by : str or list, default None
Only intervals with an equal value in column(s) `by` are clustered... | cluster | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def columns(self):
"""Return the column labels of the PyRanges.
Returns
-------
pandas.Index
See also
--------
PyRanges.chromosomes : return the chromosomes in the PyRanges
Examples
--------
>>> f2 = pr.data.f2()
>>> f2
... | Return the column labels of the PyRanges.
Returns
-------
pandas.Index
See also
--------
PyRanges.chromosomes : return the chromosomes in the PyRanges
Examples
--------
>>> f2 = pr.data.f2()
>>> f2
+--------------+-----------+--... | columns | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def count_overlaps(
self,
other,
strandedness=None,
keep_nonoverlapping=True,
overlap_col="NumberOverlaps",
):
"""Count number of overlaps per interval.
Count how many intervals in self overlap with those in other.
Parameters
----------
... | Count number of overlaps per interval.
Count how many intervals in self overlap with those in other.
Parameters
----------
strandedness : {"same", "opposite", None, False}, default None, i.e. auto
Whether to perform the operation on the same, opposite or no strand. Use Fal... | count_overlaps | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def coverage(
self,
other,
strandedness=None,
keep_nonoverlapping=True,
overlap_col="NumberOverlaps",
fraction_col="FractionOverlaps",
nb_cpu=1,
):
"""Count number of overlaps and their fraction per interval.
Count how many intervals in self o... | Count number of overlaps and their fraction per interval.
Count how many intervals in self overlap with those in other.
Parameters
----------
strandedness : {"same", "opposite", None, False}, default None, i.e. auto
Whether to perform the operation on the same, opposite or... | coverage | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def drop(self, drop=None, like=None):
"""Drop column(s).
If no arguments are given, all the columns except Chromosome, Start, End and Strand are
dropped.
Parameters
----------
drop : str or list, default None
Columns to drop.
like : str, default N... | Drop column(s).
If no arguments are given, all the columns except Chromosome, Start, End and Strand are
dropped.
Parameters
----------
drop : str or list, default None
Columns to drop.
like : str, default None
Regex-string matching columns to... | drop | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def drop_duplicate_positions(self, strand=None, keep="first"):
"""Return PyRanges with duplicate postion rows removed.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to take strand-information into account when considering duplicates.
keep : ... | Return PyRanges with duplicate postion rows removed.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to take strand-information into account when considering duplicates.
keep : {"first", "last", False}
Whether to keep first, last or drop ... | drop_duplicate_positions | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def extend(self, ext, group_by=None):
"""Extend the intervals from the ends.
Parameters
----------
ext : int or dict of ints with "3" and/or "5" as keys.
The number of nucleotides to extend the ends with.
If an int is provided, the same extension is applied to ... | Extend the intervals from the ends.
Parameters
----------
ext : int or dict of ints with "3" and/or "5" as keys.
The number of nucleotides to extend the ends with.
If an int is provided, the same extension is applied to both
the start and end of intervals, ... | extend | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def five_end(self):
"""Return the five prime end of intervals.
The five prime end is the start of a forward strand or the end of a reverse strand.
Returns
-------
PyRanges
PyRanges with the five prime ends
Notes
-----
Requires the PyRanges... | Return the five prime end of intervals.
The five prime end is the start of a forward strand or the end of a reverse strand.
Returns
-------
PyRanges
PyRanges with the five prime ends
Notes
-----
Requires the PyRanges to be stranded.
See A... | five_end | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def head(self, n=8):
"""Return the n first rows.
Parameters
----------
n : int, default 8
Return n rows.
Returns
-------
PyRanges
PyRanges with the n first rows.
See Also
--------
PyRanges.tail : return the la... | Return the n first rows.
Parameters
----------
n : int, default 8
Return n rows.
Returns
-------
PyRanges
PyRanges with the n first rows.
See Also
--------
PyRanges.tail : return the last rows
PyRanges.sample ... | head | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def insert(self, other, loc=None):
"""Add one or more columns to the PyRanges.
Parameters
----------
other : Series, DataFrame or dict
Data to insert into the PyRanges. `other` must have the same number of rows as the PyRanges.
loc : int, default None, i.e. after la... | Add one or more columns to the PyRanges.
Parameters
----------
other : Series, DataFrame or dict
Data to insert into the PyRanges. `other` must have the same number of rows as the PyRanges.
loc : int, default None, i.e. after last column of PyRanges.
Insertion i... | insert | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def intersect(self, other, strandedness=None, how=None, invert=False, nb_cpu=1):
"""Return overlapping subintervals.
Returns the segments of the intervals in self which overlap with those in other.
Parameters
----------
other : PyRanges
PyRanges to intersect.
... | Return overlapping subintervals.
Returns the segments of the intervals in self which overlap with those in other.
Parameters
----------
other : PyRanges
PyRanges to intersect.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
W... | intersect | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def join(
self,
other,
strandedness=None,
how=None,
report_overlap=False,
slack=0,
suffix="_b",
nb_cpu=1,
apply_strand_suffix=None,
preserve_order=False,
):
"""Join PyRanges on genomic location.
Parameters
-----... | Join PyRanges on genomic location.
Parameters
----------
other : PyRanges
PyRanges to join.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyRanges on the same strand, the opposite or ignore strand
info... | join | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def k_nearest(
self,
other,
k=1,
ties=None,
strandedness=None,
overlap=True,
how=None,
suffix="_b",
nb_cpu=1,
apply_strand_suffix=None,
):
"""Find k nearest intervals.
Parameters
----------
other : PyRan... | Find k nearest intervals.
Parameters
----------
other : PyRanges
PyRanges to find nearest interval in.
k : int or list/array/Series of int
Number of closest to return. If iterable, must be same length as PyRanges.
ties : {None, "first", "last", "diffe... | k_nearest | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def lengths(self, as_dict=False):
"""Return the length of each interval.
Parameters
----------
as_dict : bool, default False
Whether to return lengths as Series or dict of Series per key.
Returns
-------
Series or dict of Series with the lengths of... | Return the length of each interval.
Parameters
----------
as_dict : bool, default False
Whether to return lengths as Series or dict of Series per key.
Returns
-------
Series or dict of Series with the lengths of each interval.
See Also
---... | lengths | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def max_disjoint(self, strand=None, slack=0, **kwargs):
"""Find the maximal disjoint set of intervals.
Parameters
----------
strand : bool, default None, i.e. auto
Find the max disjoint set separately for each strand.
slack : int, default 0
Consider in... | Find the maximal disjoint set of intervals.
Parameters
----------
strand : bool, default None, i.e. auto
Find the max disjoint set separately for each strand.
slack : int, default 0
Consider intervals within a distance of slack to be overlapping.
Retu... | max_disjoint | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def merge(self, strand=None, count=False, count_col="Count", by=None, slack=0):
"""Merge overlapping intervals into one.
Parameters
----------
strand : bool, default None, i.e. auto
Only merge intervals on same strand.
count : bool, default False
Count... | Merge overlapping intervals into one.
Parameters
----------
strand : bool, default None, i.e. auto
Only merge intervals on same strand.
count : bool, default False
Count intervals in each superinterval.
count_col : str, default "Count"
Na... | merge | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def nearest(
self,
other,
strandedness=None,
overlap=True,
how=None,
suffix="_b",
nb_cpu=1,
apply_strand_suffix=None,
):
"""Find closest interval.
Parameters
----------
other : PyRanges
PyRanges to find nea... | Find closest interval.
Parameters
----------
other : PyRanges
PyRanges to find nearest interval in.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyRanges on the same strand, the opposite or ignore strand
... | nearest | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def new_position(self, new_pos, columns=None):
"""Give new position.
The operation join produces a PyRanges with two pairs of start coordinates and two pairs of
end coordinates. This operation uses these to give the PyRanges a new position.
Parameters
----------
new_pos... | Give new position.
The operation join produces a PyRanges with two pairs of start coordinates and two pairs of
end coordinates. This operation uses these to give the PyRanges a new position.
Parameters
----------
new_pos : {"union", "intersection", "swap"}
Change of... | new_position | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def overlap(self, other, strandedness=None, how="first", invert=False, nb_cpu=1):
"""Return overlapping intervals.
Returns the intervals in self which overlap with those in other.
Parameters
----------
other : PyRanges
PyRanges to find overlaps with.
stran... | Return overlapping intervals.
Returns the intervals in self which overlap with those in other.
Parameters
----------
other : PyRanges
PyRanges to find overlaps with.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to ... | overlap | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def print(self, n=8, merge_position=False, sort=False, formatting=None, chain=False):
"""Print the PyRanges.
Parameters
----------
n : int, default 8
The number of rows to print.
merge_postion : bool, default False
Print location in same column to sav... | Print the PyRanges.
Parameters
----------
n : int, default 8
The number of rows to print.
merge_postion : bool, default False
Print location in same column to save screen space.
sort : bool or str, default False
Sort the PyRanges before ... | print | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def sample(self, n=8, replace=False):
"""Subsample arbitrary rows of PyRanges.
If n is larger than length of PyRanges, replace must be True.
Parameters
----------
n : int, default 8
Number of rows to return
replace : bool, False
Reuse rows.
... | Subsample arbitrary rows of PyRanges.
If n is larger than length of PyRanges, replace must be True.
Parameters
----------
n : int, default 8
Number of rows to return
replace : bool, False
Reuse rows.
Examples
--------
>>> gr ... | sample | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def set_intersect(self, other, strandedness=None, how=None, new_pos=False, nb_cpu=1):
"""Return set-theoretical intersection.
Like intersect, but both PyRanges are merged first.
Parameters
----------
other : PyRanges
PyRanges to set-intersect.
strandedness... | Return set-theoretical intersection.
Like intersect, but both PyRanges are merged first.
Parameters
----------
other : PyRanges
PyRanges to set-intersect.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyR... | set_intersect | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def set_union(self, other, strandedness=None, nb_cpu=1):
"""Return set-theoretical union.
Parameters
----------
other : PyRanges
PyRanges to do union with.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyR... | Return set-theoretical union.
Parameters
----------
other : PyRanges
PyRanges to do union with.
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyRanges on the same strand, the opposite or ignore strand
... | set_union | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def sort(self, by=None, nb_cpu=1):
"""Sort by position or columns.
Parameters
----------
by : str or list of str, default None
Column(s) to sort by. Default is Start and End.
Special value "5" can be provided to sort by 5': intervals on + strand are sorted in as... | Sort by position or columns.
Parameters
----------
by : str or list of str, default None
Column(s) to sort by. Default is Start and End.
Special value "5" can be provided to sort by 5': intervals on + strand are sorted in ascending order, while
those on - st... | sort | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def spliced_subsequence(self, start=0, end=None, by=None, strand=None, **kwargs):
"""Get subsequences of the intervals, using coordinates mapping to spliced transcripts (without introns)
The returned intervals are subregions of self, cut according to specifications.
Start and end are relative t... | Get subsequences of the intervals, using coordinates mapping to spliced transcripts (without introns)
The returned intervals are subregions of self, cut according to specifications.
Start and end are relative to the 5' end: 0 means the leftmost nucleotide for + strand
intervals, while it means ... | spliced_subsequence | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def split(self, strand=None, between=False, nb_cpu=1):
"""Split into non-overlapping intervals.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to ignore strand information if PyRanges is stranded.
between : bool, default False
Inc... | Split into non-overlapping intervals.
Parameters
----------
strand : bool, default None, i.e. auto
Whether to ignore strand information if PyRanges is stranded.
between : bool, default False
Include lengths between intervals.
nb_cpu: int, default 1
... | split | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def stranded(self):
"""Whether PyRanges has (valid) strand info.
Note
----
A PyRanges can have invalid values in the Strand-column. It is not considered stranded.
See Also
--------
PyRanges.strands : return the strands
Examples
--------
... | Whether PyRanges has (valid) strand info.
Note
----
A PyRanges can have invalid values in the Strand-column. It is not considered stranded.
See Also
--------
PyRanges.strands : return the strands
Examples
--------
>>> d = {'Chromosome': ['ch... | stranded | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def strands(self):
"""Return strands.
Notes
-----
If the strand-column contains an invalid value, [] is returned.
See Also
--------
PyRanges.stranded : whether has valid strand info
Examples
--------
>>> d = {'Chromosome': ['chr1', 'c... | Return strands.
Notes
-----
If the strand-column contains an invalid value, [] is returned.
See Also
--------
PyRanges.stranded : whether has valid strand info
Examples
--------
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6],
... | strands | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def subset(self, f, strand=None, **kwargs):
"""Return a subset of the rows.
Parameters
----------
f : function
Function which returns boolean Series equal to length of df.
strand : bool, default None, i.e. auto
Whether to do operations on chromosome/str... | Return a subset of the rows.
Parameters
----------
f : function
Function which returns boolean Series equal to length of df.
strand : bool, default None, i.e. auto
Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use
... | subset | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def subsequence(self, start=0, end=None, by=None, strand=None, **kwargs):
"""Get subsequences of the intervals.
The returned intervals are subregions of self, cut according to specifications.
Start and end are relative to the 5' end: 0 means the leftmost nucleotide for + strand
interval... | Get subsequences of the intervals.
The returned intervals are subregions of self, cut according to specifications.
Start and end are relative to the 5' end: 0 means the leftmost nucleotide for + strand
intervals, while it means the rightmost one for - strand.
This method also allows to ... | subsequence | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def subtract(self, other, strandedness=None, nb_cpu=1):
"""Subtract intervals.
Parameters
----------
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyRanges on the same strand, the opposite or ignore strand
informati... | Subtract intervals.
Parameters
----------
strandedness : {None, "same", "opposite", False}, default None, i.e. auto
Whether to compare PyRanges on the same strand, the opposite or ignore strand
information. The default, None, means use "same" if both PyRanges are strand... | subtract | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def summary(self, to_stdout=True, return_df=False):
"""Return info.
Count refers to the number of intervals, the rest to the lengths.
The column "pyrange" describes the data as is. "coverage_forward" and "coverage_reverse"
describe the data after strand-specific merging of overlapping ... | Return info.
Count refers to the number of intervals, the rest to the lengths.
The column "pyrange" describes the data as is. "coverage_forward" and "coverage_reverse"
describe the data after strand-specific merging of overlapping intervals.
"coverage_unstranded" describes the data aft... | summary | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def tail(self, n=8):
"""Return the n last rows.
Parameters
----------
n : int, default 8
Return n rows.
Returns
-------
PyRanges
PyRanges with the n last rows.
See Also
--------
PyRanges.head : return the firs... | Return the n last rows.
Parameters
----------
n : int, default 8
Return n rows.
Returns
-------
PyRanges
PyRanges with the n last rows.
See Also
--------
PyRanges.head : return the first rows
PyRanges.sample :... | tail | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def tile(self, tile_size, overlap=False, strand=None, nb_cpu=1):
"""Return overlapping genomic tiles.
The genome is divided into bookended tiles of length `tile_size` and one is returned per
overlapping interval.
Parameters
----------
tile_size : int
Length ... | Return overlapping genomic tiles.
The genome is divided into bookended tiles of length `tile_size` and one is returned per
overlapping interval.
Parameters
----------
tile_size : int
Length of the tiles.
overlap : bool, default False
Add column... | tile | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def to_example(self, n=10):
"""Return as dict.
Used for easily creating examples for copy and pasting.
Parameters
----------
n : int, default 10
Number of rows. Half is taken from the start, the other half from the end.
See Also
--------
Py... | Return as dict.
Used for easily creating examples for copy and pasting.
Parameters
----------
n : int, default 10
Number of rows. Half is taken from the start, the other half from the end.
See Also
--------
PyRanges.from_dict : create PyRanges from... | to_example | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def three_end(self):
"""Return the 3'-end.
The 3'-end is the start of intervals on the reverse strand and the end of intervals on the
forward strand.
Returns
-------
PyRanges
PyRanges with the 3'.
See Also
--------
PyRanges.five_end ... | Return the 3'-end.
The 3'-end is the start of intervals on the reverse strand and the end of intervals on the
forward strand.
Returns
-------
PyRanges
PyRanges with the 3'.
See Also
--------
PyRanges.five_end : return the five prime end
... | three_end | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def to_bed(self, path=None, keep=True, compression="infer", chain=False):
r"""Write to bed.
Parameters
----------
path : str, default None
Where to write. If None, returns string representation.
keep : bool, default True
Whether to keep all columns, not... | Write to bed.
Parameters
----------
path : str, default None
Where to write. If None, returns string representation.
keep : bool, default True
Whether to keep all columns, not just Chromosome, Start, End,
Name, Score, Strand when writing.
c... | to_bed | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def to_bigwig(
self,
path=None,
chromosome_sizes=None,
rpm=True,
divide=None,
value_col=None,
dryrun=False,
chain=False,
):
"""Write regular or value coverage to bigwig.
Note
----
To create one bigwig per strand, subse... | Write regular or value coverage to bigwig.
Note
----
To create one bigwig per strand, subset the PyRanges first.
Parameters
----------
path : str
Where to write bigwig.
chromosome_sizes : PyRanges or dict
If dict: map of chromosome na... | to_bigwig | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def to_rle(self, value_col=None, strand=None, rpm=False, nb_cpu=1):
"""Return as RleDict.
Create collection of Rles representing the coverage or other numerical value.
Parameters
----------
value_col : str, default None
Numerical column to create RleDict from.
... | Return as RleDict.
Create collection of Rles representing the coverage or other numerical value.
Parameters
----------
value_col : str, default None
Numerical column to create RleDict from.
strand : bool, default None, i.e. auto
Whether to treat strands... | to_rle | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def unstrand(self):
"""Remove strand.
Note
----
Removes Strand column even if PyRanges is not stranded.
See Also
--------
PyRanges.stranded : whether PyRanges contains valid strand info.
Examples
--------
>>> d = {'Chromosome': ['chr... | Remove strand.
Note
----
Removes Strand column even if PyRanges is not stranded.
See Also
--------
PyRanges.stranded : whether PyRanges contains valid strand info.
Examples
--------
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6],
... | unstrand | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def window(self, window_size, strand=None):
"""Return overlapping genomic windows.
Windows of length `window_size` are returned.
Parameters
----------
window_size : int
Length of the windows.
strand : bool, default None, i.e. auto
Whether to do... | Return overlapping genomic windows.
Windows of length `window_size` are returned.
Parameters
----------
window_size : int
Length of the windows.
strand : bool, default None, i.e. auto
Whether to do operations on chromosome/strand pairs or chromosomes. ... | window | python | pyranges/pyranges | pyranges/pyranges_main.py | https://github.com/pyranges/pyranges/blob/master/pyranges/pyranges_main.py | MIT |
def rename_core_attrs(df, ftype, rename_attr=False):
"""Deduplicate columns from GTF attributes that share names
with the default 8 columns by appending "_attr" to each name if
rename_attr==True. Otherwise throw an error informing user of
formatting issues.
Parameters
----------
df : pandas... | Deduplicate columns from GTF attributes that share names
with the default 8 columns by appending "_attr" to each name if
rename_attr==True. Otherwise throw an error informing user of
formatting issues.
Parameters
----------
df : pandas DataFrame
DataFrame from read_gtf
ftype : str... | rename_core_attrs | python | pyranges/pyranges | pyranges/readers.py | https://github.com/pyranges/pyranges/blob/master/pyranges/readers.py | MIT |
def read_bam(f, sparse=True, as_df=False, mapq=0, required_flag=0, filter_flag=1540):
"""Return bam file as PyRanges.
Parameters
----------
f : str
Path to bam file
sparse : bool, default True
Whether to return only.
as_df : bool, default False
Whether to return as ... | Return bam file as PyRanges.
Parameters
----------
f : str
Path to bam file
sparse : bool, default True
Whether to return only.
as_df : bool, default False
Whether to return as pandas DataFrame instead of PyRanges.
mapq : int, default 0
Minimum mapping qua... | read_bam | python | pyranges/pyranges | pyranges/readers.py | https://github.com/pyranges/pyranges/blob/master/pyranges/readers.py | MIT |
def read_gtf(
f,
full=True,
as_df=False,
nrows=None,
duplicate_attr=False,
rename_attr=False,
ignore_bad: bool = False,
):
"""Read files in the Gene Transfer Format.
Parameters
----------
f : str
Path to GTF file.
full : bool, default True
Whether to r... | Read files in the Gene Transfer Format.
Parameters
----------
f : str
Path to GTF file.
full : bool, default True
Whether to read and interpret the annotation column.
as_df : bool, default False
Whether to return as pandas DataFrame instead of PyRanges.
nrows : int... | read_gtf | python | pyranges/pyranges | pyranges/readers.py | https://github.com/pyranges/pyranges/blob/master/pyranges/readers.py | MIT |
def read_gtf_restricted(f, skiprows, as_df=False, nrows=None):
"""seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID,... | seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the e... | read_gtf_restricted | python | pyranges/pyranges | pyranges/readers.py | https://github.com/pyranges/pyranges/blob/master/pyranges/readers.py | MIT |
def read_gff3(f, full=True, annotation=None, as_df=False, nrows=None):
"""Read files in the General Feature Format.
Parameters
----------
f : str
Path to GFF file.
full : bool, default True
Whether to read and interpret the annotation column.
as_df : bool, default False
... | Read files in the General Feature Format.
Parameters
----------
f : str
Path to GFF file.
full : bool, default True
Whether to read and interpret the annotation column.
as_df : bool, default False
Whether to return as pandas DataFrame instead of PyRanges.
nrows : i... | read_gff3 | python | pyranges/pyranges | pyranges/readers.py | https://github.com/pyranges/pyranges/blob/master/pyranges/readers.py | MIT |
def fdr(p_vals):
"""Adjust p-values with Benjamini-Hochberg.
Parameters
----------
data : array-like
Returns
-------
Pandas.DataFrame
DataFrame where values are order of data.
Examples
--------
>>> d = {'Chromosome': ['chr3', 'chr6', 'chr13'], 'Start': [146419383, 3... | Adjust p-values with Benjamini-Hochberg.
Parameters
----------
data : array-like
Returns
-------
Pandas.DataFrame
DataFrame where values are order of data.
Examples
--------
>>> d = {'Chromosome': ['chr3', 'chr6', 'chr13'], 'Start': [146419383, 39800100, 24537618], 'End... | fdr | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def fisher_exact(tp, fp, fn, tn, pseudocount=0):
"""Fisher's exact for contingency tables.
Computes the hypotheses two-sided, less and greater at the same time.
The odds-ratio is
Parameters
----------
tp : array-like of int
Top left square of contingency table (true positives).
... | Fisher's exact for contingency tables.
Computes the hypotheses two-sided, less and greater at the same time.
The odds-ratio is
Parameters
----------
tp : array-like of int
Top left square of contingency table (true positives).
fp : array-like of int
Top right square of cont... | fisher_exact | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def mcc(grs, genome=None, labels=None, strand=False, verbose=False):
"""Compute Matthew's correlation coefficient for PyRanges overlaps.
Parameters
----------
grs : list of PyRanges
PyRanges to compare.
genome : DataFrame or dict, default None
Should contain chromosome sizes. By ... | Compute Matthew's correlation coefficient for PyRanges overlaps.
Parameters
----------
grs : list of PyRanges
PyRanges to compare.
genome : DataFrame or dict, default None
Should contain chromosome sizes. By default, end position of the
rightmost intervals are used as proxies... | mcc | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def rowbased_spearman(x, y):
"""Fast row-based Spearman's correlation.
Parameters
----------
x : matrix-like
2D numerical matrix. Same size as y.
y : matrix-like
2D numerical matrix. Same size as x.
Returns
-------
numpy.array
Array with same length as input... | Fast row-based Spearman's correlation.
Parameters
----------
x : matrix-like
2D numerical matrix. Same size as y.
y : matrix-like
2D numerical matrix. Same size as x.
Returns
-------
numpy.array
Array with same length as input, where values are P-values.
Se... | rowbased_spearman | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def rowbased_pearson(x, y):
"""Fast row-based Pearson's correlation.
Parameters
----------
x : matrix-like
2D numerical matrix. Same size as y.
y : matrix-like
2D numerical matrix. Same size as x.
Returns
-------
numpy.array
Array with same length as input, ... | Fast row-based Pearson's correlation.
Parameters
----------
x : matrix-like
2D numerical matrix. Same size as y.
y : matrix-like
2D numerical matrix. Same size as x.
Returns
-------
numpy.array
Array with same length as input, where values are P-values.
See... | rowbased_pearson | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def rowbased_rankdata(data):
"""Rank order of entries in each row.
Same as SciPy rankdata with method=mean.
Parameters
----------
data : matrix-like
The data to find order of.
Returns
-------
Pandas.DataFrame
DataFrame where values are order of data.
Examples
... | Rank order of entries in each row.
Same as SciPy rankdata with method=mean.
Parameters
----------
data : matrix-like
The data to find order of.
Returns
-------
Pandas.DataFrame
DataFrame where values are order of data.
Examples
--------
>>> x = np.random.ra... | rowbased_rankdata | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def simes(df, groupby, pcol, keep_position=False):
"""Apply Simes method for giving dependent events a p-value.
Parameters
----------
df : pandas.DataFrame
Data to analyse with Simes.
groupby : str or list of str
Features equal in these columns will be merged with Simes.
pco... | Apply Simes method for giving dependent events a p-value.
Parameters
----------
df : pandas.DataFrame
Data to analyse with Simes.
groupby : str or list of str
Features equal in these columns will be merged with Simes.
pcol : str
Name of column with p-values.
keep_p... | simes | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def forbes(self, other, chromsizes, strandedness=None):
"""Compute Forbes coefficient.
Ratio which represents observed versus expected co-occurence.
Described in ``Forbes SA (1907): On the local distribution of certain Illinois fishes: an essay in statistical ecology.``
Parameters
... | Compute Forbes coefficient.
Ratio which represents observed versus expected co-occurence.
Described in ``Forbes SA (1907): On the local distribution of certain Illinois fishes: an essay in statistical ecology.``
Parameters
----------
other : PyRanges
Intervals to ... | forbes | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def jaccard(self, other, **kwargs):
"""Compute Jaccards coefficient.
Ratio of the intersection and union of two sets.
Parameters
----------
other : PyRanges
Intervals to compare with.
chromsizes : int, dict, DataFrame or PyRanges
Integer repre... | Compute Jaccards coefficient.
Ratio of the intersection and union of two sets.
Parameters
----------
other : PyRanges
Intervals to compare with.
chromsizes : int, dict, DataFrame or PyRanges
Integer representing genome length or mapping from chromosom... | jaccard | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def relative_distance(self, other, **kwargs):
"""Compute spatial correllation between two sets.
Metric which describes relative distance between each interval in one
set and two closest intervals in another.
Parameters
----------
other : PyRanges
Intervals ... | Compute spatial correllation between two sets.
Metric which describes relative distance between each interval in one
set and two closest intervals in another.
Parameters
----------
other : PyRanges
Intervals to compare with.
chromsizes : int, dict, DataFra... | relative_distance | python | pyranges/pyranges | pyranges/statistics.py | https://github.com/pyranges/pyranges/blob/master/pyranges/statistics.py | MIT |
def from_string(s, int64=False):
"""Create a PyRanges from multiline string.
Parameters
----------
s : str
String with data.
int64 : bool, default False.
Whether to use 64-bit integers for starts and ends.
See Also
--------
pyranges.from_dict : create a PyRanges fro... | Create a PyRanges from multiline string.
Parameters
----------
s : str
String with data.
int64 : bool, default False.
Whether to use 64-bit integers for starts and ends.
See Also
--------
pyranges.from_dict : create a PyRanges from a dictionary.
Examples
------... | from_string | python | pyranges/pyranges | pyranges/__init__.py | https://github.com/pyranges/pyranges/blob/master/pyranges/__init__.py | MIT |
def itergrs(prs, strand=None, keys=False):
r"""Iterate over multiple PyRanges at once.
Parameters
----------
prs : list of PyRanges
PyRanges to iterate over.
strand : bool, default None, i.e. auto
Whether to iterate over strands. If True, all PyRanges must be stranded.
keys ... | Iterate over multiple PyRanges at once.
Parameters
----------
prs : list of PyRanges
PyRanges to iterate over.
strand : bool, default None, i.e. auto
Whether to iterate over strands. If True, all PyRanges must be stranded.
keys : bool, default False
Return tuple with ke... | itergrs | python | pyranges/pyranges | pyranges/__init__.py | https://github.com/pyranges/pyranges/blob/master/pyranges/__init__.py | MIT |
def random(n=1000, length=100, chromsizes=None, strand=True, int64=False, seed=None):
"""Return PyRanges with random intervals.
Parameters
----------
n : int, default 1000
Number of intervals.
length : int, default 100
Length of intervals.
chromsizes : dict or DataFrame, def... | Return PyRanges with random intervals.
Parameters
----------
n : int, default 1000
Number of intervals.
length : int, default 100
Length of intervals.
chromsizes : dict or DataFrame, default None, i.e. use "hg19"
Draw intervals from within these bounds.
strand : bo... | random | python | pyranges/pyranges | pyranges/__init__.py | https://github.com/pyranges/pyranges/blob/master/pyranges/__init__.py | MIT |
def to_bigwig(gr, path, chromosome_sizes):
"""Write df to bigwig.
Must contain the columns Chromosome, Start, End and Score. All others are ignored.
Parameters
----------
path : str
Where to write bigwig.
chromosome_sizes : PyRanges or dict
If dict: map of chromosome names t... | Write df to bigwig.
Must contain the columns Chromosome, Start, End and Score. All others are ignored.
Parameters
----------
path : str
Where to write bigwig.
chromosome_sizes : PyRanges or dict
If dict: map of chromosome names to chromosome length.
Examples
--------
... | to_bigwig | python | pyranges/pyranges | pyranges/__init__.py | https://github.com/pyranges/pyranges/blob/master/pyranges/__init__.py | MIT |
def _handle_eval_return(self, result, col, as_pyranges, subset):
"""Handle return from eval.
If col is set, add/update cols. If subset is True, use return series to subset PyRanges.
Otherwise return PyRanges or dict of data."""
if as_pyranges:
if not result:
return pr.PyRanges()
... | Handle return from eval.
If col is set, add/update cols. If subset is True, use return series to subset PyRanges.
Otherwise return PyRanges or dict of data. | _handle_eval_return | python | pyranges/pyranges | pyranges/methods/call.py | https://github.com/pyranges/pyranges/blob/master/pyranges/methods/call.py | MIT |
def sort_one_by_one(d, col1, col2):
"""
Equivalent to pd.sort_values(by=[col1, col2]), but faster.
"""
d = d.sort_values(by=[col2])
return d.sort_values(by=[col1], kind="mergesort") |
Equivalent to pd.sort_values(by=[col1, col2]), but faster.
| sort_one_by_one | python | pyranges/pyranges | pyranges/methods/sort.py | https://github.com/pyranges/pyranges/blob/master/pyranges/methods/sort.py | MIT |
def _introns_correct(full, genes, exons, introns, by):
"""Testing that introns:
1: ends larger than starts
2: the intersection of the computed introns and exons per gene are 0
3: that the number of introns overlapping each gene is the same as number of introns per gene
4 & 5: that the intron positi... | Testing that introns:
1: ends larger than starts
2: the intersection of the computed introns and exons per gene are 0
3: that the number of introns overlapping each gene is the same as number of introns per gene
4 & 5: that the intron positions are the same as the ones computed with the slow, but corre... | _introns_correct | python | pyranges/pyranges | tests/unit/test_genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/tests/unit/test_genomicfeatures.py | MIT |
def test_introns_single():
"Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single"
gr = pr.data.gencode_gtf()[["gene_id", "Feature"]]
exons = gr[gr.Feature == "exon"].merge(by="gene_id")
exons.Feature = "exon"
exons = exons.df
df = pd.co... | Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single | test_introns_single | python | pyranges/pyranges | tests/unit/test_genomicfeatures.py | https://github.com/pyranges/pyranges/blob/master/tests/unit/test_genomicfeatures.py | MIT |
def makecube():
""" Generate vertices & indices for a filled cube """
vtype = [('a_position', np.float32, 3),
('a_texcoord', np.float32, 2)]
itype = np.uint32
# Vertices positions
p = np.array([[1, 1, 1], [-1, 1, 1], [-1, -1, 1], [1, -1, 1],
[1, -1, -1], [1, 1, -1], ... | Generate vertices & indices for a filled cube | makecube | python | timctho/VNect-tensorflow | vispy_test.py | https://github.com/timctho/VNect-tensorflow/blob/master/vispy_test.py | Apache-2.0 |
def _create_base_cipher(dict_parameters):
"""This method instantiates and returns a handle to a low-level
base cipher. It will absorb named parameters in the process."""
use_aesni = dict_parameters.pop("use_aesni", True)
try:
key = dict_parameters.pop("key")
except KeyError:
raise ... | This method instantiates and returns a handle to a low-level
base cipher. It will absorb named parameters in the process. | _create_base_cipher | python | mchristopher/PokemonGo-DesktopMap | app/pylibs/osx64/Cryptodome/Cipher/AES.py | https://github.com/mchristopher/PokemonGo-DesktopMap/blob/master/app/pylibs/osx64/Cryptodome/Cipher/AES.py | MIT |
def new(key, mode, *args, **kwargs):
"""Create a new AES cipher
:Parameters:
key : byte string
The secret key to use in the symmetric cipher.
It must be 16 (*AES-128*), 24 (*AES-192*), or 32 (*AES-256*)
bytes long.
Only in `MODE_SIV`, it needs to be 32, 48, or 64 bytes lo... | Create a new AES cipher
:Parameters:
key : byte string
The secret key to use in the symmetric cipher.
It must be 16 (*AES-128*), 24 (*AES-192*), or 32 (*AES-256*)
bytes long.
Only in `MODE_SIV`, it needs to be 32, 48, or 64 bytes long.
mode : a *MODE_** constant
... | new | python | mchristopher/PokemonGo-DesktopMap | app/pylibs/osx64/Cryptodome/Cipher/AES.py | https://github.com/mchristopher/PokemonGo-DesktopMap/blob/master/app/pylibs/osx64/Cryptodome/Cipher/AES.py | MIT |
def _create_base_cipher(dict_parameters):
"""This method instantiates and returns a handle to a low-level
base cipher. It will absorb named parameters in the process."""
try:
key = dict_parameters.pop("key")
except KeyError:
raise TypeError("Missing 'key' parameter")
effective_keyl... | This method instantiates and returns a handle to a low-level
base cipher. It will absorb named parameters in the process. | _create_base_cipher | python | mchristopher/PokemonGo-DesktopMap | app/pylibs/osx64/Cryptodome/Cipher/ARC2.py | https://github.com/mchristopher/PokemonGo-DesktopMap/blob/master/app/pylibs/osx64/Cryptodome/Cipher/ARC2.py | MIT |
def __init__(self, key, *args, **kwargs):
"""Initialize an ARC4 cipher object
See also `new()` at the module level."""
if len(args) > 0:
ndrop = args[0]
args = args[1:]
else:
ndrop = kwargs.pop('drop', 0)
if len(key) not in key_size:
... | Initialize an ARC4 cipher object
See also `new()` at the module level. | __init__ | python | mchristopher/PokemonGo-DesktopMap | app/pylibs/osx64/Cryptodome/Cipher/ARC4.py | https://github.com/mchristopher/PokemonGo-DesktopMap/blob/master/app/pylibs/osx64/Cryptodome/Cipher/ARC4.py | MIT |
Subsets and Splits
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Filters Python code examples from Django repository that contain Django-related code, helping identify relevant code snippets for understanding Django framework usage patterns.
SQL Console for Shuu12121/python-treesitter-filtered-datasetsV2
Retrieves specific code examples from the Flask repository but doesn't provide meaningful analysis or patterns beyond basic data retrieval.
HTTPX Repo Code and Docstrings
Retrieves specific code examples from the httpx repository, which is useful for understanding how particular libraries are used but doesn't provide broader analytical insights about the dataset.
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Retrieves code examples with their docstrings and file paths from the requests repository, providing basic filtering but limited analytical value beyond finding specific code samples.
Quart Repo Docstrings & Code
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