sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4ce3e503f7e4c84bddc770ec9c61355575a61390296c69ac2094673850da127d | Python | 2,671 | 78 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import numpy as np
import torch
import json
from fairseq import utils
from fairseq.models.text_to_speech.vocoder import CodeHiFiGANVocoder
#... |
7b039d3b1850d56be8dad63b4af1c67555f2ff93b947fb12bef0a30a01816f04 | Python | 2,671 | 81 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from packaging.utils import canonicalize_name
from poetry.factory import Factory
from poetry.repositories import Repository
if TYPE_CHECKING:
from tests.types import PackageFactory
@pytest.fixture
def repo() -> Repository:
... |
2801fb9a4c78a7e30c31ce1bfd0b9083563e80362799afd701f62253fb966f3e | Python | 2,672 | 67 | #!/usr/bin/env python
import argparse
import torch
from .layers import v2_positional_encoding as v2
# def main():
# parser = argparse.ArgumentParser()
# parser.add_argument("--inverse", action="store_true", help="Inverse the tone curve")
# parser.add_argument("--no-grad", action="store_false", des... |
04b728a94422f7eef3af9febfcf7d0f292c49931584e8e87c7472722727ab325 | Python | 2,673 | 106 | """
This is a modified version of the code present in:
https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/reformat_consensus.py
"""
import argparse
import logging
import sys
import os
import pysam
def parse_args(argv):
"""
Commandline parser
:param argv: Command li... |
be123a0d40a563bdd8d4697fe51c6599f2800039399ce128f220a377d16c1e23 | Python | 2,673 | 79 | # @license
# Copyright 2020 Google Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... |
7ea029cdddd7849bb2a79353ea9c54b278e53b2f76f92222a5615b7262b3d331 | Python | 2,674 | 81 | __author__ = 'Robbert Harms'
__date__ = '2017-10-23'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class NumDiffInfo:
"""Encapsulates information necessary for numerical differentiation of a parameter."""
@property
def max_step(self):
"""Get the maximum nu... |
d9d5ca240a8bed7986d3e55a45b2e6d08dab35cdcada321e8e05c59391cc6018 | Python | 2,674 | 69 | import logging
import shlex
import sys
from unittest.mock import patch
import pytest
from gsMap.main import main
def parse_bash_command(command: str) -> list[str]:
"""Convert multi-line bash command to argument list for sys.argv"""
cleaned_command = command.replace("\\\n", " ")
cleaned_command = " ".joi... |
dedc12bf1812cb093e2ccad82cfed95fcd12917552af95044223a8c42fddb18f | Python | 2,674 | 75 | import logging
from typing import Any
from pydantic import root_validator
from pydantic.main import BaseModel
class BulkRNABertConfig(BaseModel):
n_genes: int
n_expressions_bins: int
embed_dim: int
init_gene_embed_dim: int
project_gene_embedding: bool = False
use_gene_embedding: bool = True
... |
6cd8635d94fed2883b9d4bbbb943b27cef2d53988097ee34bada6b6a0d2f5e99 | Python | 2,677 | 108 | """
Misc wrappers for some VTK classes.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from vtk.util.vtkConstants import VTK_ID_TYPE
from .base import BSVTKObjectWrapper
from ..decorators import unwrap_input, wrap_output
class BSCollection(BSVTKObjectWrapper):
"""Wrapper for... |
7a5c4287bb68328aeea310915e2ee4c7c57c0d37c80fcdcfa7786e49a2ed3ed4 | Python | 2,678 | 84 | import os
import zarr
import tskit
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
from tqdm import tqdm
from multiprocessing import Pool
import glob
# get number of windows from glob
# TODO: maybe change this from glob to look at the zarr directly
tree_files = glob.glob(o... |
b5e0640f11ce1ad0207696e3292caffe70ac4dae6c029c5e162cf14abe3360e2 | Python | 2,678 | 82 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import os
import numpy as np
import cv2
from MLPerf_cal_images import get_cal_fns
from ... |
93ae4c47792ba7aadd141c7228145add272e0dcc7736602cf8e7a6814ae52ef9 | Python | 2,680 | 40 | from predify.modules import PCoderN
from predify.networks import PNetSeparateHP
from torch.nn import Sequential, ReLU, ConvTranspose2d
class PVGG16SeparateHP(PNetSeparateHP):
def __init__(self, backbone, build_graph=False, random_init=False, ff_multiplier=(0.2,0.4,0.4,0.4), fb_multiplier=(0.05,0.1,0.1,0.1), er_mul... |
a0c02d49eecf2bea2269764d4164783e81b5f360de09f629eaac1b7b36d2d80a | Python | 2,680 | 75 | """
06_tissue_enrichment.py
Brain vs. blood tissue enrichment comparison.
Computes PCDH co-expression in GTEx whole blood (n=755) and compares
with brain regions.
Harbert D. (2026) BMC Genomics
"""
import sys, os
sys.path.insert(0, os.path.dirname(__file__))
from utils import *
def main():
ensure_dirs()
cac... |
20e96f2f18de0a068b962a4c2f583b908460a24bf72ef7a85518bcac841148aa | Python | 2,681 | 79 | import unittest
from unittest.mock import patch
from pyecharts import options as opts
from pyecharts.charts import Kline
data = [
[2320.26, 2320.26, 2287.3, 2362.94],
[2300, 2291.3, 2288.26, 2308.38],
[2295.35, 2346.5, 2295.35, 2345.92],
[2347.22, 2358.98, 2337.35, 2363.8],
[2360.75, 2382.48, 2347... |
3cbbdbb4753449d33f799f69f0dbd5d504907bd1316061597f77f7a6b90e8345 | Python | 2,681 | 88 | from mdt import CompositeModelTemplate
import numpy as np
__author__ = 'Robbert Harms'
__date__ = "2015-06-22"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
class BallStick_r1(CompositeModelTemplate):
model_expression = '''
S0 * ( (Weight(w_ball) * Ball) +
(Weight(w_stick... |
785e2fefda2fe0ec3e55b088ad6af403c9bb5e740efa2ece8c88584425f7d391 | Python | 2,682 | 85 | """Utility functions that streamline preparing vertex arrays for plotting"""
import os
import numpy as np
DATA = os.path.abspath(os.path.join(os.path.dirname(__file__), 'data'))
def add_fslr_medial_wall(data, split=False):
"""Add medial wall to data in fsLR space
Data in 32k fs_LR space (e.g., Human Connect... |
4ec600ab7af0a2ea407bb8ad52d640f9030dc70691f5c5b6af4d914b77190cef | Python | 2,683 | 73 | import os
from os.path import join, basename, dirname
import pandas as pd
from matplotlib import pyplot as plt
from config_path import PLOTS_PATH, PROSTATE_LOG_PATH
base_dir = join(PROSTATE_LOG_PATH, 'review/fusion')
files = []
files.append(dict(Model='Fusion', file=join(base_dir, 'onsplit_average_reg_10_tanh_large... |
7f956e2d98fa2e07f6fb3a7fc657a54368f38f6aaa250c899327e7b2bec7b519 | Python | 2,683 | 91 | import pandas as pd
import pytest
from mock import MagicMock, Mock, call
from pgmpy.estimators import BIC
from pgmpy.estimators.ScoreCache import LRUCache, ScoreCache
def test_caching():
function_mock = Mock(side_effect=[1, 2])
cache = LRUCache(function_mock, max_size=2)
assert cache("key1") == 1
as... |
1618d60bfe6431600c6b0a182193806853fef2d399b422f2199a4ca07f20aca6 | Python | 2,684 | 80 | #!/usr/bin/env python3
"""Unit tests for SIVmac split-read fixtures (no Nextflow)."""
import glob
import os
import sys
import tempfile
import unittest
REPO = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.insert(0, os.path.join(REPO, "bin"))
from filter_reads import parse_args, filter_reads, is_... |
86feafa0c9f6aa12dd3b53121f782a49c75a4e28a17fac831a83617bdf1fe8f2 | Python | 2,685 | 70 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class ThemeRiver(Chart):
"""
<<< ThemeRiver >>>
ThemeRiver graph is a special kind of flow graph,
which is mainly used to show the changes of events or themes
over ... |
914639b4587f79396e8b9da7d42e2e3f3d4e6e065661789522016b53fbc3a24e | Python | 2,685 | 79 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
import numpy as np
import re
from pathlib import Path
from collections import defaultdict
import pandas as pd
... |
d6c4616f7c6c24620621a6abc007f8b0ad1ede703ad84f08b9377d23bee57c97 | Python | 2,685 | 85 | from time import sleep
from pathlib import Path
import mne_bids
import pylossless as ll
def load_openneuro_bids(subject="pd6", timeout=20):
"""Download and Load BIDS dataset ds002778 from OpenNeuro.
Parameters
----------
subject : str
The subject to load. Defaults to ``"pd6"``.
Returns... |
ca1124ad251a83b24e90fb662ac6dd86cbc320318c66c2221a1ddea8afe0fdba | Python | 2,687 | 103 | import functools
import time
import torch
import torch.autograd as autograd
import torch.cuda.comm as comm
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd.function import once_differentiable
class CA_Weight(autograd.Function):
@staticmethod
def forward(ctx, t, f):
# Save con... |
049a5546fb3f6620d79f70ccda0ae76fd091e710c0a261d717d3ddfe5acb2ea5 | Python | 2,688 | 90 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import option
from poetry.console.commands.command import Command
if TYPE_CHECKING:
from cleo.io.inputs.option import Option
from poetry.utils.env import Env
class EnvInfoCommand(Command):
... |
173340855ad89499eafbf9c7fc65e07aea9ec5b6235ba14452c77a00e1906949 | Python | 2,689 | 70 | import torch
import torchvision.ops
from torch import nn
class DeformableConv2d(nn.Module):
def __init__(self,
in_channels,
out_channels,
kernel_size=3,
stride=1,
padding=1,
bias=False):
supe... |
d9684922a884f7f40a94fe5839e21acf9bf15c07c61c848386b62e6a5bdab40d | Python | 2,691 | 84 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import typing as tp
def _safe_readline(fd) -> str:
pos = fd.tell()
while True:
try:
return fd.readline... |
24816d08696ca51cc1f5f623d55ba5677a7ff767f0c3cc4d38b013a7226a6266 | Python | 2,695 | 101 | """Top-level GOATOOLS command-line dispatcher."""
from __future__ import print_function
import importlib
import sys
from goatools import __version__
SUBCOMMANDS = {
"compare_gos": (
"goatools.cli.compare_gos",
"Compare two or more sets of GO IDs.",
),
"fetch_associations": (
"go... |
0fa8cb54e58beeeea4254bd21d4457d11557da590b4106a6fff85dfa71e82786 | Python | 2,697 | 91 | import npyx
from npyx.c4.dataset_init import get_paths_from_dir, extract_and_check
from npyx.c4.acg_vs_firing_rate import main as acg_main
from npyx.c4.dataset_init import save_features
import pandas as pd
import npyx.feat as feat
import numpy as np
import os
from celltype_ibl.params.config import DATASETS_DIRECTORY
#... |
07f90b1cc44e09fd4737d278c9897ac6136f0ddd15d152c502bf387555de7036 | Python | 2,698 | 76 | """Smoke tests for the minimal pattern-analysis upload.
Recompute a few reported values and assert them. Read the original data via
`source: server`; skip cleanly if the data is not mounted.
pytest -q # fast
pytest -q -m slow # + permutation / atlas-loading checks
"""
import numpy as np
import pandas... |
0216992e4263cd2285c088a825af363d3c1949c1ccad78e879e79c8c51ff0148 | Python | 2,700 | 86 | from __future__ import annotations
from pathlib import Path
from .df_common import detect_photometry_file_type, expected_analysis_output_path
from .df_dual import compute_dual_options, run_dual_analysis
from .df_single import compute_single_options, run_single_analysis
def run_analysis(
selectedfile: str | Path... |
446610946a1a6feb18744960bf96857d77e5e678afacb21d20d64b1541e62982 | Python | 2,704 | 80 | #!/usr/bin/env python
# ENCODE DCC blacklist filter wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
import multiprocessing
from encode_common import *
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC Blacklist filter.',
... |
54031ba80260ba1132ded1c492c6a29c9a2c4468d4eacc0ae6631f5406a4369e | Python | 2,704 | 63 | #!/usr/bin/env python3
import polars as pl
import argparse
from src.utils import read_fasta, write_fasta, read_gtf, collapse_isoforms_to_proteoforms
def main():
parser = argparse.ArgumentParser(description='Filter genome_gffs from TransDecoder with novel transripts')
parser.add_argument('--mode', action='... |
7d1c4a49307411defeee1d08e6d06176aebd8b40f34b61cf22954979bff33292 | Python | 2,704 | 79 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from ...cores.analog_core import AnalogCore
from scipy.linalg import dft
clas... |
95ef3893fd230b42b8cc199337435e320a670c0da3a6ca562c87a8ee69945242 | Python | 2,705 | 90 | import os
from random import randint
APP_NAME = '%s-%d' % ('fashion-mnist', randint(0, 100))
LOG_FORMAT = '%(asctime)-15s %(filename)s:%(funcName)s:[%(levelname)s] %(message)s'
JSON_FORMAT = '%(message)s'
RUN_LOCALLY = False
ROOT_DIR = os.path.dirname(os.path.abspath(__file__)) + '/'
TEST_DIR = ROOT_DIR + 'test/'
DAT... |
96079c97453c8d2de8adedaeccf49273545c6a01b4c91f14ee35788988e80e32 | Python | 2,707 | 80 | import os
import numpy as np
def create_dir(path : str):
# create directory if it doesn't exist
if not os.path.exists(path):
os.makedirs(path)
# 3D euclidean rotation around the y-axis
def Ry3D(θ : float) -> np.ndarray:
return np.array([
[np.cos(θ), 0, np.sin(θ)],
[0, 1, 0],
... |
1a4c49eef20aeba21b959baa04f5a15c6a71e5d6eeac5d7ea0933a038d1da0da | Python | 2,708 | 79 | import os
from copy import deepcopy
from os.path import dirname
import numpy as np
from model.builders.prostate_models import build_dense
base_dirname = dirname(dirname(__file__))
print (base_dirname)
filename = os.path.basename(__file__)
task = 'classification_binary'
# need to stired under 'data/genes'
selected_ge... |
7f0e943fa30e6fde17cd24f3a6bbf374223f331cca9be9c3a0d4c9b69e2a2337 | Python | 2,708 | 74 | #!/usr/bin/env python3
import argparse
import csv
from collections import defaultdict
def parse_args():
parser = argparse.ArgumentParser(description="Summarize UMI stats from multiple stats files.")
parser.add_argument("stats_files", nargs="+", help="Input stats .tsv files (one or more)")
parser.add_argume... |
91bae3f0f127be6ad5ee425410e688aea3866a99295d6604a02544a96da2ba03 | Python | 2,708 | 89 | # -*- coding: utf-8 -*-
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
cb414a443ee70fcb121820ee222244c65e9091fcccedbb2cb0819ff7187ad480 | Python | 2,709 | 70 | from mdt import CompartmentTemplate, FreeParameterTemplate
from mdt.model_building.parameter_functions.transformations import ScaleTransform
__author__ = 'Robbert Harms'
__date__ = '2018-09-15'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class GDRCylinders(CompartmentTempla... |
7276d5a94c754083401caed07de9f94e7bfd9bc02b3ea74ff1b884b706200484 | Python | 2,710 | 73 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
e57febc59ecb70ee7418ac45600cab7fc4cd409b4eead0e886f44176b6b728ff | Python | 2,713 | 71 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
0da09c646c3e70bba619b5fc0c74fc302226eaa808824ae9e4a58bc554d72094 | Python | 2,714 | 61 | import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.patches import FancyBboxPatch, FancyArrowPatch
plt.rcParams.update({"font.family": "DejaVu Sans"})
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(16, 7.6),
gridspec_kw={"width_ratios": [1.08, 1.0]})
#... |
c95301261e65ce697102e84488b21421c75ab4650a18215b3507949470981213 | Python | 2,714 | 91 | #!/usr/bin/env python3 -u
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import hydra
import torch
from hydra.core.hydra_config import HydraConfig
from omegaconf i... |
a24702e73d1cffc4f1b7ea33c1beff0f59512a8fdaa457a6cc84fcc0dd6c61b8 | Python | 2,715 | 87 | import itertools
import os
import platform
from cffi import FFI
dir_path = os.path.dirname(os.path.realpath(__file__))
#samver is pulled from this file in the Makefile
samver = "1.20"
htslib_dir = os.path.join(dir_path, 'submodules', 'samtools-{}'.format(samver), 'htslib-{}'.format(samver))
deflatever = "1.10"
defla... |
e5e7013c30ce13993046fb6ec66af32a02617938bbe0fc2109512583e7411fe6 | Python | 2,716 | 58 | """Validate browser-generated ZIPs with the unchanged desktop/Colab reader."""
import json
from pathlib import Path
import sys
import tempfile
import numpy as np
from PIL import Image
ROOT = Path(__file__).resolve().parents[2]
sys.path[:0] = [str(ROOT / "SegRef3D"), str(ROOT / "ColabNotebooks"), str(ROOT / "ColabNote... |
245afef0c314f8096b4569b99156f939a7e84d35a94ba9b6a053bad0db6aca94 | Python | 2,719 | 79 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
from . import BaseWrapperDataset, data_utils
from fairseq.data.text_compressor import TextCompressor, TextCompressionLevel
cla... |
9933b9bbb66cdbc427ee8f72847fb60784be75879de8d5da1c716eea53a1386b | Python | 2,719 | 86 | import os
from utils.paths import ROOT_DIR
# --- Define Valid Network Names ---
# These are names of the different CNN architecture classes defined in ROOT_DIR/src/networks/cnn.py
# While there are sevetal CNN architecture classes defined in cnn.py, only a few (e.g. "BINND") are relevant for BINND
VALID_NETWORK_NAMES ... |
f262b14a6d76a11ad932e34c3c5f6e67472a226d6d750c8de849197ac4357407 | Python | 2,719 | 75 | """Inference-API tests for hippie.inference.HIPPIEClassifier.
These tests exercise the public inference surface without requiring a
real pretrained checkpoint. Network-dependent tests (from_pretrained on
HuggingFace Hub) are marked with the `network` pytest marker.
"""
from __future__ import annotations
from pathlib... |
2a1c1daaf1ba435a9c4aadc2464a9219bd387786f8292f9d269f77da589a9b7b | Python | 2,720 | 51 | """Sensitivity of the fruit-juice results to the disputed composition entry for sample p59.
The spreadsheet records p59 as 65 % orange juice; the sample-coding scheme (100 - 5n, followed by
all 54 other samples) implies 55 %. The analysis uses 55 %. This script re-runs the fruit-juice
benchmark both ways so the depend... |
61033455f89e515a6f5703ea2d31e8c2a024d56e0e3d0b953fca97179892e9a2 | Python | 2,721 | 93 | from abc import ABC, abstractmethod
from typing import Dict, Optional
import importlib
import os
import numpy as np
class AudioTransform(ABC):
@classmethod
@abstractmethod
def from_config_dict(cls, config: Optional[Dict] = None):
pass
class CompositeAudioTransform(AudioTransform):
def _from_... |
0b47c680aa1a444032ecfb56dd5540b0db854031f424c0d4d6ef0b968c6b0ad1 | Python | 2,725 | 90 | """`brenda_references.scripts` must import without the root's dev group.
Its `__init__` installs beartype's import hook, and beartype is declared by no
runtime dependency anywhere in the tree, so every module there was importable
purely as a side effect of a developer install. The probe runs in a subprocess
because th... |
486ec3a8d3ee5aa9e9082055ec75664f058c95d67c23e6abb58afe6d5d7f1d03 | Python | 2,725 | 60 | #!/usr/bin/env python
"""Script for generation table with data/models from list.json in .md format"""
import argparse
import json
DATASETS_SOURCE = "list.json"
def generate_table(fn):
with open(fn) as infile:
data = json.loads(infile.read())
datasets = sorted(data["corpora"].items(), key=lambda kv:... |
9e644b39fa4e38059fc253928796c61219b1f6b60f49e403f954150c6fdd8b12 | Python | 2,726 | 64 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
1d8b2e23a25e5841e4cfa68b7b9f8ac82de542ffb4c54de245bf3bda1b31102a | Python | 2,730 | 87 | import matplotlib.pyplot as plt
import numpy as np
# Function to read data from a file and calculate mean, min, and max
def calculate_stats(file_path):
with open('./date/'+file_path, 'r') as file:
data = [float(line.strip()) for line in file if line.strip()]
mean = np.mean(data)
min_val = n... |
3b6423b39f55d9007926e3fada95b740c697a028b80939976e5932304425bc86 | Python | 2,734 | 84 | from typing import List, Tuple
import re
from itertools import product, zip_longest
import pandas as pd
import numpy as np
_FASTA_VOCAB = "ARNDCQEGHILKMFPSTWYV"
def single_mutant_names(sequence: str) -> List[str]:
"""Returns the names of all single mutants of a sequence."""
mutants = []
for (i, wt), mut ... |
7eb7b88960f77a4fa36e90b443c0e446a0f0c05bfc9f1edce593312e37fb8148 | Python | 2,734 | 88 | import matplotlib.pyplot as plt
import numpy as np
import loompy
from .colors import colorize
from .scatter import scatterc, scattern
def batch_covariates(ds: loompy.LoomConnection, out_file: str) -> None:
xy = ds.ca.TSNE
plt.figure(figsize=(12, 12))
if "Tissue" in ds.ca:
names, labels = np.unique(ds.ca.Tissu... |
8032e56cd6115d8e928423dd71c2ea7c7d9987011dbb91be984aae5681e5e290 | Python | 2,734 | 101 | from __future__ import annotations
import locale
import sys
import warnings
from contextlib import suppress
from pathlib import Path
if sys.version_info < (3, 11):
# compatibility for python <3.11
import tomli as tomllib
else:
import tomllib
from importlib import metadata as _metadata
WINDOWS = sys.p... |
1da5487dd9bd29612b2e10dc1e681140ebc8a8f494c9825a42cb3c6df644c691 | Python | 2,735 | 65 | import json
import os
import urllib.request
import numpy as np
from oneqmc.molecule import Molecule
if __name__ == "__main__":
data_dir = os.path.join(os.path.dirname(__file__), os.pardir, "data")
reference_energy_dir = os.path.join(
os.path.dirname(__file__), os.pardir, "experiment_results", "03_tin... |
7e82bc3d749974fad15b1c0a4fac28ffa795779e8d34186172e2a54633c6081d | Python | 2,735 | 88 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# Adapted from examples/wav2vec/wav2vec_manifest.py
"""
Data preparation for the speech normalizer
"""
import argpars... |
bd57eead9498cdb01266847de3f8812d03cf885c8380b029cd3d21f3b1bcdd6f | Python | 2,736 | 91 | '''
Wrapper functions for fancy dendrograms
'''
import gzip as gzip_module
import logging
import numpy as np
import os
import pandas as pd
import pathlib
import shlex
import shutil
import subprocess
def fancy_dendrogram(
distances,
clusters,
map,
outdir,
outfile,
... |
eef22c82217d074af122f4ec4ae627b90f0224f8d6f2977a7a250ca91de93949 | Python | 2,737 | 65 | from mdt import LibraryFunctionTemplate
__author__ = 'Robbert Harms, Francisco J. Fritz'
__date__ = "2015-06-21"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
class SSFP(LibraryFunctionTemplate):
"""Implementation of the SSFP signal attenuation.
This uses the algorithm described in:
"T... |
1bbd38dc29664ddc5262d8e7e933fca2d3a3fc3c4e65f0ec54ba087ee454d4f3 | Python | 2,741 | 58 | #!/usr/bin/env python3
"""Make sure that all of the schemas are correct by testing them on known good and bad inputs."""
# flake8: noqa: T201
import json
import os
import argparse
import jsonschema
import bpreveal.schema as schemas
from bpreveal.internal import interpreter
p = argparse.ArgumentParser(description="Check... |
ec050d049e3651a106dc84204ff4737e1a729884a47121eed04cece142479fe9 | Python | 2,741 | 61 | import cv2 as cv
import numpy as np
#选取一幅图片，
def Draw_Save_Border(rootpath,borderimgpath):
img = cv.imread(borderimgpath,flags=-1)
a,b = [],[]
def on_EVENT_LBUTTONDOWN(event, x, y, flags, param):
if event == cv.EVENT_LBUTTONDOWN:
xy = "%d,%d" % (x, y)
a.append(x)
... |
12fa03bbea122dde23b456a564079954ff58ff735712d4127e50264879955685 | Python | 2,742 | 77 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
python %prog study.file population.file gene-association.file
This program returns P-values for functional enrichment in a cluster of
study genes using Fisher's exact test, and corrected for multiple testing
(including Bonferroni, Holm, Sidak, and false discovery rate... |
43c2bec8d763b167ed742fdc9b9d207627b433c51194a4026078901842e50bae | Python | 2,743 | 85 | import os
from typing import Optional, Any
from collections import defaultdict
from simulation_encoder.logger import Logger
from simulation_encoder.loaders.loader import Loader
class AlphanumericLoader(Loader):
"""Loader class for loading labeled images from a directory."""
def __init__(
self,
... |
eb07e52f1142f170bd28582190af520a29885b4fbc0bcb595e76e4f02c779f34 | Python | 2,743 | 65 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
from fairseq import utils
from fairseq.modules import TransformerEncoderLayer
from .multihead_linear_attention import MultiheadL... |
a3930f850c696364b43f34dd9779fcff05e0d6d3a9787f806efde136d4d85a68 | Python | 2,744 | 88 | #
# utils.py
# Copyright (c) 2020 Daisuke Endo
# This software is released under the MIT License.
# http://opensource.org/licenses/mit-license.php
#
#----------------------------------
# 作成者：Daisuke Endo
# 連絡先:daisuke.endo96@gmail.com
# 最終更新日 2020/5/17
#----------------------------------
# ここには3つの関数を記述している。
# 1. ファイルの読... |
beaf6caf5bf5bb63817a54f87cc4e1d247b1f913d0264a859c0ad11d5d3117cf | Python | 2,747 | 91 | from typing import Literal
import torch
from torchmetrics import Metric
class ElboMetric(Metric):
"""Elbo metric aggregator for scvi-tools experiments.
Parameters
----------
name
Name of metric, used as the prefix of the logged name.
mode
Train or validation, used as the suffix o... |
0b8e82ed55ae022f0eb52e46184f276429c75937de113c721f67926100345441 | Python | 2,748 | 63 | #!/home/s/shreejoy/nxu/miniforge3/envs/patch_seq_spl/bin/python
import polars as pl
import argparse
from src.utils import read_fasta, write_fasta, read_gtf, collapse_isoforms_to_proteoforms
def main():
parser = argparse.ArgumentParser(description='Filter genome_gffs from TransDecoder with novel transripts')
... |
b96aecc62da7992dd673b0bac547bcc30a48f0281ca39e3cb4a1467a6bbb48af | Python | 2,751 | 69 | """Featurize the SIESTA-PBE-relaxed polymorphs with OCE Wave-1.5.
Mirrors featurize.py but reads the relaxed geometries from
siesta_production_results.json (instead of the xtb results). Formal charges
(A=+2, B=+4, O=-2) are pulled from the original structures.json by name.
Writes feat_siesta/features_combined.npz for ... |
229821055fdd6602c2be0f8b283d1e043a6fe0239ca483ab90de27d099d5f5bc | Python | 2,754 | 81 | """Visualize the category distribution in the selected stimuli."""
# Imports
import os
import click
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from datasets import load_from_disk
from scipy.stats import chi2_contingency
from compositionality_study.constants import COCO_SELECTED_STIMULI... |
935ca4cdec25a70e8bff4dad977d1e1e6e73bcff668c5c8bf82e7caae14a61a8 | Python | 2,754 | 87 | """
Logic to generate sobol samples for analysing A\beta Reelin dynamics based on the related
parameters. Sequences to enable second order analysis are generated.
"""
from SALib.analyze import sobol
from SALib.sample.sobol import sample
import numpy as np
from scipy.stats import qmc
## RE
# alpha_base 4680... |
06b1586aa25725836bfff0e1c5e5b362aa8dec690621efd0ab043f197f3c0c4a | Python | 2,756 | 69 | import logging
import shutil
from pathlib import Path
from .. import config, learncurve
from ..common.logging import config_logging_for_cli, log_version
from ..common.paths import generate_results_dir_name_as_path
logger = logging.getLogger(__name__)
def learning_curve(toml_path):
"""generate learni... |
1e6990568bad858fc8a3d9c2b703befc86cee5c9597a0fc41b578702d691998b | Python | 2,757 | 83 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
from dataclasses import dataclass, field
from typing import Optional
import torch
from .dummy_dataset import DummyDataset
from... |
a43b90d333aeeb7422d7a95d568330bca1a2244bb82f608d928288ff023ade7c | Python | 2,757 | 71 | from collections.abc import Sequence
from typing import Optional
import jax
import jax.numpy as jnp
from ....geom import masked_pairwise_diffs, norm
def psiformer_masked_pairwise_diffs(
x: jax.Array,
y: jax.Array,
x_mask: jax.Array,
y_mask: jax.Array,
*,
eps: float = 1e-26,
) -> tuple[jax.Ar... |
8bf8b6e3ae5e67cac0f2d31d545e624d89d8a7769c2f07aa43dd27235190462f | Python | 2,760 | 83 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from dataclasses import dataclass, field
from typing import List
from omegaconf import II
from fairseq.dataclass import FairseqD... |
25d88b410d33b6828dd8bb389e91e72640df3eb664d6b9fb7f2bc31b44a4860b | Python | 2,761 | 61 | import os
import tempfile
import unittest
import numpy as np
from medaka.common import Region, Sample
from medaka import datastore
class TestStore(unittest.TestCase):
@classmethod
def setUpClass(cls):
pos = np.array([(0, 0), (0, 1), (1, 0), (2, 0), (2, 1), (2, 2), (3, 0), (4, 0), (4, 1), (4, 2), (4... |
64708adb2fb2cbfed56ed5b425f0db540a4f7c4cec0193be835ec9ab027e6aa2 | Python | 2,761 | 85 | import time
import numpy as np
from omegaconf import DictConfig, OmegaConf
import torch
from pathlib import Path
import os
import json
import copy
import argparse
import random
# from torch.nn.parallel import DistributedDataParallel as DDP
# from torch.distributed import init_process_group, destroy_process_group
from... |
d4b40afeb9cb572fa1f6039123b69ac74957121c9d24e01f9594567e37b69175 | Python | 2,761 | 67 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os, sys
import subprocess
import re
from subprocess import check_call, check_output
WORKDIR_ROOT = os.environ.get('WORKDIR_ROOT', Non... |
400038e5e20279bb2523e4710a6f6bdb316622e09cefe40eeb9c4d13bc4501e6 | Python | 2,762 | 67 | # from data_specific.Proc_TS_Dataset import Get_TS_Datasets, Save_TSImgDatasetInfo, Load_TSImgDatasetInfo
# from data_specific.Proc_Features import Save_Features_FromTSDatasets
# from data_specific.Proc_TSImgs import Save_TSImgs_FromTSDatasets, Load_TSImgs_PT
# from LibKIME.LibML import Split_Dataset_PT
import sy... |
967cec40286871c5e99ea83cc56712c0d4759aba91a8f03bbcd0c26a3400a174 | Python | 2,763 | 101 | import pandas as pd
import pytest
from pgmpy.models import DiscreteBayesianNetwork
from pgmpy.structure_score import (
AICCondGauss,
AICGauss,
BICCondGauss,
BICGauss,
LogLikelihoodCondGauss,
LogLikelihoodGauss,
)
@pytest.fixture
def small_df():
return pd.DataFrame(data={"A": [0, 0, 1], "B... |
4a098c3a2de5db5454e1db68011fdf2ebd798a9e38de5519aa4a677d83f54715 | Python | 2,767 | 80 | import unittest
from unittest.mock import patch
from pyecharts.charts import Bar
from pyecharts.render.engine import RenderEngine
from pyecharts.datasets import EXTRA, FILENAMES
from pyecharts.globals import CurrentConfig
class TestEngine(unittest.TestCase):
def test_generate_js_link(self):
FILENAMES.up... |
4fe4cec5d9a65616204d6e72714b4f317f1f993b22a4a287a53c180c85f06e11 | Python | 2,768 | 103 | """
Copyright (c) Facebook, Inc. and its affiliates.
Copyright (c) Microsoft Corporation.
Licensed under the MIT License.
Adapted from https://github.com/FAIR-Chem/fairchem/blob/main/src/fairchem/core/models/gemnet/layers/embedding_block.py.
"""
import numpy as np
import torch
from mattergen.common.gemnet.layers.base... |
ee78ae920bcd7b2bb1cdea1abcd59126a58c5dd145723a558757b1bff28166f2 | Python | 2,768 | 70 | from os.path import join
from config_path import PATHWAY_PATH
from model.builders.prostate_models import build_pnet_KEGG
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_genes_and_cancer_genes.csv'
data_base = {'id': 'ALL', 'type': 'prostate_paper',
'params': {
'd... |
f960369560b2e3acc0acc4ca23a93babeb55b74d26096ecfd0017370e8e1272c | Python | 2,769 | 77 | import vtk, qt, slicer
from math import sqrt, cos, sin
from slicer.util import VTKObservationMixin
from .PointerEffect import AbstractPointerEffect
class AbstractCircleEffect(AbstractPointerEffect, VTKObservationMixin):
sphere = None
sphereModelNode = None
def __init__(self, sliceWidget):
AbstractPointer... |
06a3930bfc3e3ca2bbd9e65d3af4bd5f7c97045d95c866821906c1b43e6567ac | Python | 2,770 | 75 | import h5py
import numpy as np
import tensortools as tt
import pickle
import os
# Set parameters
num_animals = 12
replicate = 0
n_components = [3]
total_runs = 100
for run in range(0, total_runs):
print('Replicate: ', run+1)
print('\n')
output_dir = f"tca_factors"
os.makedirs(output_dir, exist_ok=Tru... |
878276fc499527cef9c5c58ab8f771cbeb06e0f3db5745cffdadb31d3231e230 | Python | 2,771 | 88 | """Helper functions for working with datasets represented as a pandas.DataFrame"""
from __future__ import annotations
import pathlib
import numpy as np
import pandas as pd
def get_dataset_csv_filename(data_dir_name: str, timenow: str) -> str:
"""Get name of csv file representing dataset.
This function is ... |
192865c236b6c71c542c199f2b8e962ed04df1d3c6f442a5e55a55294da6c945 | Python | 2,772 | 76 | import unittest
from types import SimpleNamespace
from unittest.mock import patch
from GMXMMPBSA import make_top
from GMXMMPBSA.exceptions import MMPBSA_Error
class RequireComplexTopologyTest(unittest.TestCase):
def _checker(self, **file_overrides):
files = SimpleNamespace(
complex_tpr='com.t... |
c305d5ee1610e5f27e3e76d38bca3a29ac18b51cd7d69fd894e8085f77a525af | Python | 2,772 | 63 | import attrs
@attrs.define
class ConfigMetadata:
"""Dataclass that represents metadata
about a configuration file
Attributes
----------
filename : str
The name of the configuration file.
model : str
The name of the model in :mod:`vak`
that the configuration file is use... |
c7e630a4dc4737a08a684bbc58301dbdf9c66507e69d55e810ab8ce6de9b9d64 | Python | 2,773 | 64 | import torch.nn as nn
from ..layers.convolutions import Convolutional
class Residual_block(nn.Module):
def __init__(self, filters_in, filters_out, filters_medium):
super(Residual_block, self).__init__()
self.__conv1 = Convolutional(filters_in=filters_in, filters_out=filters_medium, kernel_size=1,
... |
f9cac1ad2fbeb37801aab7b617b350aaec3c788beb77eceb98cb70c06f780a58 | Python | 2,774 | 75 | import h5py
import numpy as np
import tensortools as tt
import pickle
import os
# Set parameters
num_animals = 12
replicate = 0
n_components = [3]
total_runs = 100
for run in range(0, total_runs):
print('Replicate: ', run+1)
print('\n')
output_dir = f"tca_factors"
os.makedirs(output_dir, exist_ok=Tru... |
99d85d8565e1f03874eebaca2f70624337d507f81ba2bdcbdec55d198f2031df | Python | 2,775 | 95 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import csv
import io
import logging
import os
import os.path as op
import sys
from dump_hubert_feature import HubertFeatureReader
from featur... |
559f634312722234a47cc5f9b235a721790aefd9fbd557ea2b6310edd0d599d1 | Python | 2,779 | 77 | import os
from os.path import join, basename, dirname
import pandas as pd
from matplotlib import pyplot as plt
from config_path import PLOTS_PATH, PROSTATE_LOG_PATH
base_dir = join(PROSTATE_LOG_PATH, 'review/cnv_burden_training')
files = []
files.append(
dict(Model='P-NET with CNV burden', file=join(base_dir, ... |
f65dbcd67eb2dbfee8859d81aab1825795f698192c4339903c547637ca51d907 | Python | 2,779 | 92 | import json
import re
import unicodedata
from examples.mms.data_prep.norm_config import norm_config
def text_normalize(text, iso_code, lower_case=True, remove_numbers=True, remove_brackets=False):
"""Given a text, normalize it by changing to lower case, removing punctuations, removing words that only contain di... |
3829578f6632314699be17d6f12a9aceaaaacdb510b66dd4c99f7f6be38d79e4 | Python | 2,780 | 85 | from __future__ import annotations
from logging import LogRecord
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from poetry.console.logging.io_formatter import IOFormatter
from poetry.console.logging.io_formatter import _log_prefix
from poetry.console.logging.io_formatter import _path_to_pac... |
0804004b881bb4fc08358ddde0caca4261f532cbd6f10bf7079cac23911f491a | Python | 2,781 | 96 | """Regression test for the dropped `store_strains` await in `sync_doc_db`."""
import asyncio
from apiadapters.straininfo import AsyncStrainInfoAdapter
from apiadapters.straininfo.straininfo import StrainRef
from brenda_references import brenda_references as bref
from brenda_references import db as db_module
from bre... |
67336b4d5812f53e7e94e401227fbf9245af3ae17b98cfa7bbf60cfd1c042e42 | Python | 2,781 | 83 | import colour
import numpy as np
from matplotlib import rcParams
from matplotlib.colors import Colormap, LinearSegmentedColormap
def set_axes():
rcParams["axes.spines.right"] = False
rcParams["axes.spines.top"] = False
rcParams["axes.edgecolor"] = "black"
def set_figure():
rcParams["fig... |
bcdea719fe6ada7d53a82a644728eb9ac73d1a0d74a64feb1871df9ad59c12df | Python | 2,782 | 76 | # -*- coding: utf-8 -*-
import os
import gc
import argparse
import json
import random
import math
import random
from functools import reduce
import numpy as np
import pandas as pd
from scipy import sparse
from sklearn.model_selection import train_test_split, ShuffleSplit, StratifiedShuffleSplit, StratifiedKFold
from sk... |
5eb82f8479e48599834285f21c5702823b9043ae70e5baca6c98e79951443c5c | Python | 2,783 | 84 | """Per-epoch batch-weighted metric aggregation and full-training stat history (replaces Logger.stat lists)."""
from __future__ import annotations
from collections import OrderedDict
from typing import Any, Dict, List, Optional
class RunningWeightedAverage:
def __init__(self) -> None:
self._sum... |
104859160cc41b1b99ffdcad94551012d47cc2e64f9aded3f33aeaa0b4dc6f35 | Python | 2,786 | 75 | import h5py
import numpy as np
import tensortools as tt
import pickle
import os
# Set parameters
num_animals = 12
replicate = 0
n_components = [3]
total_runs = 100
for run in range(0, total_runs):
print('Replicate: ', run+1)
print('\n')
output_dir = f"tca_factors"
os.makedirs(output_dir, exist_ok=Tru... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.