content
stringlengths
35
416k
sha1
stringlengths
40
40
id
int64
0
710k
import math def cost(a, b, c, e, f, p_min, p): """cost: fuel cost based on "standard" parameters (with valve-point loading effect) """ return a + b * p + c * p * p + abs(e * math.sin(f * (p_min - p)))
62e93d90b7a9620376ea3a91156707f5a6ef5105
676,002
import torch def coco_annotations_to_tensors(coco_annotations, image_shape, parts, topology, max_count=100): """Gets tensors corresponding to peak counts, peak coordinates, and peak to p...
d5943f974d1a6dae899449bae070e38c0239c577
676,003
def calculate_offset(address, base, shadow_base=0): """ Calculates an offset between two addresses, taking optional shadow base into consideration. Args: address (int): first address base (int): second address shadow_base (int): mask of shadow address that is applied to `base` ...
7614a1263c2d73cacf509c769e53503b80052839
676,004
import yaml def get_yaml_dict(yaml_file): """Return a yaml_dict from reading yaml_file. If yaml_file is empty or doesn't exist, return an empty dict instead.""" try: with open(yaml_file, "r") as file_: yaml_dict = yaml.safe_load(file_.read()) or {} return yaml_dict except FileNotFoundError: return {}
bf290735bc3d30f8517d8513f8d2679a1383e718
676,005
import os import subprocess import sys import traceback def execute(args, command_args): """Execute IDA Pro as a subprocess, passing this file in as a batch-mode script for IDA to run. This forwards along arguments passed to `mcsema-disass` down into the IDA script. `command_args` contains unparsed arguments pa...
3caedbf21a89604a7d016cf61cee914f60a5ea9e
676,007
import math def tand(v): """Return the tangent of x (measured in in degrees).""" return math.tan(math.radians(v))
a3023dcdf19bb7b235ac5389011c0243498b7128
676,008
def decode_to_string(data): """ :param data: :return: """ decoding = {} for k, v in data.items(): decoding[k] = v[0].decode() if type(v) == list and len(v) == 1 else [i.decode() for i in v] return decoding
83e13291ae4ae3208f8ac14cc1167d693fbf9ffd
676,009
import torch def compute_mask(x, sequence_lengths, batch_axis=0, sequence_axis=1): """ This function calculates a mask which indicates the position of non-padded values. It can be used to do subsequent operations only on non-padded values. >>> x, seq_len = 2*torch.ones((3,1,10,4)), [1, 2, 3] >>> ...
e75c2e40b5dfd76565d6fd3b72fadd151160f4b2
676,010
def misra_c2012_compare(rule): """ compare misra C2012 rules """ return int(rule.split('.')[0])*100 + int(rule.split('.')[1])
16a35130f9b3338638645d3cde9c4997034f4dde
676,011
import numpy def unDiskify(x, y, scaleR): """ Convert x y to unit disk, return the radial scale factor """ r = numpy.sqrt(x**2 + y**2) * scaleR theta = numpy.arctan2(y, x) _x = numpy.cos(theta) * r _y = numpy.sin(theta) * r return _x, _y
c5ff58021284a609429e06760b1f492cfa78f44f
676,012
def cartesian(coords): """ Convert 2D homogeneus/projective coordinates to cartesian. """ return coords[:, :2]
36566982c7d2aa9cb3fda1aeab8de1d0ee2fb115
676,013
def getObjectKey(rpcObject): """Given a rpc object, get a unique key that in the form 'class.id' @type rpcObject: grpc.Message @param rpcObject: Rpc object to get a key for @rtype: str @return: String key in the form <class>.<id> """ objectClass = rpcObject.__class__.__name__ object...
dcd1af06fcbe6022d5382eee79878ad6a222a3c5
676,014
import calendar def sort_months(months): """Sort a sequence of months by their calendar order""" month_ref = list(calendar.month_name)[1:] return sorted(months, key=lambda month: month_ref.index(month))
71c465901149f3a7dac325d3f3e97d495a245c94
676,015
def _python_command(self): """ 如果是py文件,则存成一条command """ with open(self.file_path, 'r') as f: py_string = f.read() return py_string
02516d59ea0c3618a79f97d7e2810f951cf2c406
676,016
def find_md_link_or_url(text): """ find_md_link_or_url('ab[cd](ef)xy') returns: ('abcdxy', 'ef') All the text goes into the text, and the URL as well. """ start = (0,) open_sq = (1,) closed_sq = (2,) open_curve = (3,) closed_curve = (4,) state = start text_content = ...
e7bfa888a1e08d5efc9a522f3d83b98e3ca6c1fc
676,017
from pathlib import Path import tempfile import venv def create_new_venv() -> Path: """Create a new venv. Returns: path to created venv """ # Create venv venv_dir = Path(tempfile.mkdtemp()) venv.main([str(venv_dir)]) return venv_dir
077dd1318d579ccdb3333849b092555c54297903
676,018
import os def _get_log_file_for_script(config, script_name): """Returns a path to the log file for the given script.""" logs_dir = config['logging']['logs_dir'] if not os.path.isabs(logs_dir): logs_dir = os.path.join(os.path.dirname(__file__), os.pardir, logs_dir) return os.path.join(logs_dir...
5fb34b39eab28d173413fdd37237dd0730dee5d2
676,019
def compare_files(first_list, second_list): """ Compares two lists that should contain the path + filename of the modified files. The two lists are mutable. :param first_list: First lists. :param second_list: Second list :return: returns boolean value in case a match is found. """ for e...
c388ac2c536e7650d3f0fc5becf0c6790919d9f2
676,020
import os import json def get_splits(root: str): """ Reads splits file indices.json :param root: :return: """ with open(os.path.join(root, "training_indices.json")) as f: dict = json.load(f) return dict
989dec3f980179453e3f40a5954d8c15d3ade013
676,021
def inc(x_b): """Return the pathname of the KOS root directory.""" return x_b + 1
8a57ca513d5c84233dcf7382a0d9fade3a8b8226
676,022
def total_seconds(td): """ Return total seconds in timedelta object :param td: timedelta :type td: datetime.timedelta :return: seconds :rtype: float """ return (td.microseconds + (td.seconds + td.days * 86400) * 1000000) / 1000000.0
8aab761d946bee240e2c49d5de0885f021d82ba6
676,024
def adjust_lenght(string, max_length): """Adjust the length of string.""" while len(string) > max_length: string = string[:-1] return string
e3eca0886ee1f9a85bcf3bd6c4976999613531d9
676,025
import getpass def get_mysql_pwd(config): """Get the MySQL password from the config file or an interactive prompt.""" # Two ways to get the password are supported. # # 1. Read clear-text password from config file. (least secure) # 2. Read password as entered manually from a console prompt. (most s...
3077fca733739d1d0648e555fa2a485a31cc3d8a
676,026
def postfix_to_infix(postfix: str) -> str: """ start reading from beginning 1. every operand gets pushed into the stack 2. for every operator, pop 2 operands and push (op1 op op2) back into stack 3. repeat """ stack: list = [] for c in postfix: if c.isalpha(): stack....
5e403754ccb91e4a1abf695c055ee63707299f7e
676,027
import os def is_testmode(): """Server is running in the wttr.in test mode""" return "WTTRIN_TEST" in os.environ
01ecb4d62a5563dc8c034f48c92ff2294efa388d
676,029
import six def median_from_dict(total, count): """ total is the number of requests made count is a dict {response_time: count} """ pos = (total - 1) / 2 for k in sorted(six.iterkeys(count)): if pos < count[k]: return k pos -= count[k]
d4993ffb8f140c1a3f322b19b6975a7a8fd04d95
676,030
import torch def scaled_sign(x, name=None): """ :param x: torch Tensor :return: The sign tensor scaled by it's L1 norm divided by the number of elements """ _scale = x.norm(p=1) / x.numel() _sign = torch.sign(x) return _scale, _sign
a632c7d23527fce80f2c195e5208c5a1eb629718
676,031
def deep_merge(a, b): """Merges a and b, letting b win if there is a conflict""" merged = a.copy() for key in b: b_value = b[key] merged[key] = b_value if key in a: a_value = a[key] if isinstance(a_value, dict) and isinstance(b_value, dict): me...
d5b557c155867b386e99babd14036ca7f25c05d0
676,032
def nstr(n): """Represent integer in radix with base up to 62 using digits, big letters and small letters. """ if n < 10: return str(n) n -= 10 if n < 26: return chr(ord('A') + n) n -= 26 return chr(ord('a') + n)
0c9b6ce6d974cf03a10a178a96828a9b0d854034
676,033
def resolve_attribute(name, bases, default=None): """Find the first definition of an attribute according to MRO order.""" for base in bases: if hasattr(base, name): return getattr(base, name) return default
ed358e230da7ca7bb2a413caee151f344c111b25
676,034
def findORF_all_sorted_longest_n(dna_seq, n): """ Finds all the longest open reading frames in the DNA sequence. """ tmpseq = dna_seq.upper(); orf_all = [] for i in range(0, len(tmpseq), 3): codon = tmpseq[i:i+3] if codon == 'ATG': orf = tmpseq[i:] for j i...
240d91053b8dfa925601c1004430cbfb0d120e71
676,035
def _get_date_and_time_strings(date): """Return string of YYYYMMDD and time in HHMM format for file access.""" y, m, d, h = [str(i) for i in [date.year, date.month, date.day, date.hour]] # add zeros if needed if len(m) == 1: m = '0' + m if len(d) == 1: d = '0' + d if len(h) == 1...
da60c58bd6c13e104caf2d01d479675d7d7a7b8a
676,037
import os import fnmatch def read_files(directory, pattern='*.png'): """ Recursively read a directory and return all files that match file pattern. """ matched_files = [] for root, dirs, files in os.walk(directory): # Filter only filename matches matches = [os.path.join(root, f...
1cc77a718252a72809bf57ecec0e8a94226fb636
676,038
import typing def format_scopes(scopes: typing.List[str]) -> str: """Format a list of scopes.""" return " ".join(scopes)
5776e849ff96ab250f2b957309c6b1829ac54383
676,039
import re def get_size_from_tags(tags): """Searches a tags string for a size tag and returns the size tag. Size tags: spacesuit, extrasmall, small, medium, large, extralarge. """ match = re.search( r'\b(spacesuit|extrasmall|small|medium|large|extralarge)\b', tags ) if match: re...
8d406d237a7249b6d3807af6375f56b5c124ca8b
676,040
def distance_from_camera(bbox, image_shape, real_life_size): """ Calculates the distance of the object from the camera. PARMS bbox: Bounding box [px] image_shape: Size of the image (width, height) [px] real_life_size: Height of the object in real world [cms] """ ## REFERENCE FOR GOPRO ...
037adbaba89ae13ed74ac5fc1d1cfc080c5107d1
676,041
def get_occurences(node, root): """ Count occurences of root in node. """ count = 0 for c in node: if c == root: count += 1 return count
7df5e3e1c5fbcdca482a297e38b5e09be1b3d8e1
676,042
import os def get_path(parsed_args, *args): """Return an absolute path, given a path relative to the base.""" base_path = os.path.abspath(parsed_args.base_path) return os.path.join(base_path, *args)
c90e98b85b49a70432f1881242240b333daeb9e4
676,043
import re def handle_globals(local_identifiers, global_identifiers, YoPy): """ This function handles the preceding ':' for external variables """ output = "" YoPy.seek(0, 0) for line in YoPy.readlines(): matches = re.findall(r'(:[a-z0-9]+)', line) if matches: for m ...
134f2d316b9455da1d5bcadb97c39f9e7e06c96c
676,044
import json import subprocess import os def dangerously_simulate_api_response(request_dict): """*SHOULD NOT RECEIVE USER INPUT*. Simulates the API output for the specified request using server files located within this repository's directory structure. The request should be in the form of a dictionary specifyin...
2c7f570f6f14302e44f278433ad34ea7ed6a8224
676,045
from typing import OrderedDict def remove_duplicates(text: str) -> str: """Remove duplicates from text. Function uses OrderedDict, which keeps order and distinct elements. """ set_ = OrderedDict() for x in text: set_[x] = None return ''.join(set_.keys())
c0d1d0e853cd96ca387dfae625c730eda2793858
676,046
import os import pickle def load_dataset(pickle_path,only_one=False): """Loads and returns dataset clips from pickled_path""" clips = {} if(only_one): #Loads only one pkl. Useful for testing purposes pkl = sorted(os.listdir(pickle_path))[0] clips["1"] = pickle.load(open(pickle_path...
f62ad07f3b73499f835235714f04e1f1be0b8c7e
676,047
def snd(tpl): """ >>> snd((0, 1)) 1 """ return tpl[1]
d002211609082a2c14f49b826643c774dd6205c3
676,048
from pathlib import Path from typing import List def get_regions_data(path: Path) -> List[dict]: """Gets base data for a region in a page. :param path: Path to the region directory. :return: List of dictionaries holding base region data. """ regions = list() for region in sorted(path.glob("....
b5e4d10f58815eaec23104ec37ac6c9beaa45c43
676,050
def get_members_name(member): """Check if member has a nickname on server. Args: member (Union[discord.member.Member, list]): Info about member of guild Returns: str: User's name, if user doesn't have a nickname and otherwise list: List of names of user's nicknames """ if i...
4b8798a98dc6064b775a72e44c1189408e7a0073
676,051
from typing import Callable from typing import Any from typing import Optional import inspect def has_param(fn: Callable[..., Any], name: str, pos: Optional[int] = None) -> bool: """ Inspects function fn for presence of an argument. """ args = inspect.getfullargspec(fn)[0] if name in args: ...
b4c29366a29bda65e1337301545fc4cf9b18d76c
676,052
def cgr_neighbor_function(contact_graph, node, destination, current_distance, set_visited, suppressed_contacts, lookahead_time): """Neighbor function of CGR used by the Dijkstra algorithm. Used to determine feasible direct neigbors of a given node. Args: contact_graph (C...
1a5efa908b22424d22b2b823fd0f425d4ea3d611
676,053
def to_alternating_case(string): """Input a string, return string with case swapped""" return "".join([s.swapcase() for s in string])
3e94a5fbfdaccb496fd90453f070baf8ea422f14
676,054
import re def escape_shell_chars_tmsu(str): """ escapes all chars which would cause problems in shell and also replaces / with \, because tmsu does not accept \ in tags :param str: :return: """ str = str.replace("/", "\\") str = re.sub("(!|\$|#|&|\"|\'|\(|\)|\||<|>|`|\\\|;| )", r"\\\1"...
3a8685084e639ea9c68e3bea0c99b2c23425fa4f
676,055
import os def abslistdir(directory): """ returns a list of absolute filepaths for all files found in the given directory. """ abs_dir = os.path.abspath(directory) filenames = os.listdir(abs_dir) return [os.path.join(abs_dir, filename) for filename in filenames]
9f76193e4f966c7c3f5477623ebc5d819b60dc75
676,056
def get_all_children(base_pid): """ Return all child PIDs of base_pid process :param base_pid starting PID to scan for children :return tuple of the following: pid, binary name, command line incl. binary :type base_pid int :rtype list[(int, str, str)] """ parent_pid_path_pattern = "/proc/{0}/task/{0}/...
85859188c990dec234a96e32e822293462140f7b
676,057
def find_layer_idx(model, layer_name): """Looks up the layer index corresponding to `layer_name` from `model`. Args: model: The `keras.models.Model` instance. layer_name: The name of the layer to lookup. Returns: The layer index if found. Raises an exception otherwise. """ ...
ab5c8bcde11e22aa0081a2bb60c9b99c324b6525
676,058
def _start_time_from_groupdict(groupdict): """Convert the argument hour/minute/seconds minute into a millisecond value. """ if groupdict['hours'] is None: groupdict['hours'] = 0 return (int(groupdict['hours']) * 3600 + int(groupdict['minutes']) * 60 + int(groupdict['seco...
0f09960f3cb482931445d304a963236db11c2228
676,059
def frame_to_pattern(frame_path): """Convert frame count to frame pattern in an image file path. Args: frame_path (str): Path of an image file with frame count. Returns: str: Path of an image sequence with frame pattern. """ name_list = frame_path.split('.') name_list[-2] = '%...
bfd1c973281b11295d4c17752c5ae1b2c221fad7
676,060
import math def visibility(nov, nol, a): """Compute visibility using height-correlated GGX. Heitz 2014, "Understanding the Masking-Shadowing Function in Microfacet-Based BRDFs" Args: nov: Normal dot view direction. nol: Normal dot light direction. a: Linear roughness. Returns: The geometr...
04fb867d55622951fee64c7edb22d042f890ae74
676,061
def flip(res): """flips 'x', 'o' or 'draw'.""" if res == 'x': return 'o' elif res == 'o': return 'x' elif res == 'draw': return 'draw' else: raise RuntimeError("Invalid res: %s" % str(res))
22438c63ae9cc456c2d090b2462e6277a6146d6e
676,062
def plot_info(ax, freq, label=False): """ Plots the marker for the simulated frequency Parameters ---------- For a description of the parameters see 'plot_panel_row'. """ # if label: # ax.text(freq+0.2, 0.85, f'P$_\mathrm{{sim.}}$ = {1/freq:.2f} d', # transform=ax.trans...
0a67e8191614535c9ec8b427e612ac0c5636ede8
676,063
def RotXOR(s, n, target): """ Input: Byte array 's' of size 16, integer 'n', Byte array 'target' of size 16 Output: Byte array of size 16 which is result of operation Right-rotate 's' by 'n' bits and XOR with 'target' then return the result If in any case we have to do left shift/rotate x bits ...
48c58d200bd0031f0e448b608e1a23026b188c4a
676,064
import math def calculate_tail_correction(box_legth, n_particles, cutoff): """ Calculates the tail correction Parameters ---------- box_legth : float The distance between the particles in reduced units. n_particles : int The number of particles. cutoff : float ...
16ea67d6423cf4a466313a2766aa9c9c4d7c0f15
676,065
def getPdbCifLink(pdb_code): """Returns the html path to the cif file on the pdb server """ file_name = pdb_code + '.cif' pdb_loc = 'https://files.rcsb.org/download/' + file_name return file_name, pdb_loc
ff8eebf8eb5559088e8f37be67b9b032383b2541
676,066
def prep_sub_id(sub_id_input): """Processes subscription ID Args: sub_id_input: raw subscription id Returns: Processed subscription id """ if not isinstance(sub_id_input, str): return "" if len(sub_id_input) == 0: return "" return "{" + sub_id_input.strip...
719693c2a11d1e8611fceec80b34b07a157e91ad
676,067
def ls(conn, path): """If path contains a wildcard (* or %): Return all paths known to the database that start match the given path argument (containing wildcards). If path doesn't contain wildcards: Return the exact match on the path argument.""" if path.find('*') >= 0 or path.find('%'...
cc289fe13a6d3e96a3004a7f9431ff448523f177
676,068
def list_tokenizer(tokenizer, text_list): """Split train dataset corpus to list """ line_list = list() for text in text_list: line_list.append(tokenizer.tokenize(text)) return line_list
76a2081f7ef12d5f4c571400f2669d22b52f4364
676,069
def nth_eol(src, lineno): """ Compute the ending index of the n-th line (before the newline, where n is 1-indexed) >>> nth_eol("aaa\\nbb\\nc", 2) 6 """ assert lineno >= 1 pos = -1 for _ in range(lineno): pos = src.find('\n', pos + 1) if pos == -1: return ...
d0a77d3541874d054297a78bd1307bc18ec220af
676,070
import requests def get_online_person(params=None, **kwargs) -> bytes: """Get a picture of a fictional person from the ThisPersonDoesNotExist webpage. :param params: params dictionary used by requests.get :param kwargs: kwargs used by requests.get :return: the image as bytes """ r = requests.g...
1b492fcf4d67f1431d8883af1761135d4d52cd97
676,071
def safe_pop(data, index=0, default=None): """This function pops safetly a GqlResponse from a subscription queue. Args: data (list): Is the list of GqlResponse that caught the subscription. index (int, optional): Index of the subscription queue. Defaults to 0. default (None, optional): Define the...
207a1a1acd688ea7485d5d4034b4f7cc6618d6aa
676,072
def cols_to_count(df, group, columns): """Count the number of column values when grouping by another column and return new columns in original dataframe. Args: df: Pandas DataFrame. group: Column name to groupby columns: Columns to count. Returns: Original DataFrame with ne...
d9bdb0e6a87805a02a21d7f19505e84206264d66
676,074
def node_exists(api, node_name): """Determines whether the specified node is still part of the cluster-on-aws.""" nodes = api.list_node(include_uninitialized=True, pretty=True).items node = next((n for n in nodes if n.metadata.name == node_name), None) return False if not node else True
50083fddbd767a015ec1a429cd838084c1ecb495
676,076
import hashlib import binascii def _get_hash(password): """ calculate hash on password :param password: :return hash: """ hex_hash = hashlib.pbkdf2_hmac('sha256', password.encode(), b'user', 100_000) return binascii.hexlify(hex_hash)
5d637d22ab710912cfae5525e368403890456333
676,078
import math def calcVector(p1,p2): """ calculate a line vector in polar form from two points. The return is the length of the line and the slope in degrees """ dx = p2[0]-p1[0] dy = p2[1]-p1[1] mag = math.sqrt(dx * dx + dy * dy) theta = math.atan2(dy,dx) * 180.0 / math.pi + 90.0 re...
bb89a5332aba097f6178d679accc8786b3e07d51
676,079
def striplines(text): """ Remove all leading/trailing whitespaces from lines and blank lines. """ return "\n".join( line.strip() for line in text.splitlines() if len(line.strip()) )
d0122580daa2e0bff8be323b2eeb1f7966b86cf0
676,080
def hop(context): """multi-lines string""" return ['''<a id="sendbutton" href="javascript: $('%(domid)s').submit()"> <img src="%(sendimgpath)s" alt="%(send)s"/>%(send)s</a>''' % context, '''<a id="cancelbutton" href="javascript: history.back()"> <img src="%(cancelimgpath)s" alt="%(cancel)s"/>%(cance...
9ad98fd5007dbae3f62440e463b94e65244af3da
676,081
def combine(background_img, figure_img): """ Erase the green screen in figure_img and combine the result 'figure' with 'space_ship'. :param background_img: the background image to place 'figure' :param figure_img: the figure with green screen, erase the green screen in image w...
e1fa1dc4986d2d0c252a85d7830064f6153aa5d1
676,082
import os import tempfile from typing import Any def save_artifact(model: Any, filename: str): """ Parameters ---------- model The model bytes to save. filename The filename for the model Returns ------- Return the local folder """ folder = tempfile.mkdtemp() print(fold...
c5f244c48d78e209180786980781bf492f675dc7
676,083
def exchange(flw, exchanges_list): """Add docstring.""" exchanges_list.append(flw) return exchanges_list
f3823077da5dd9aeca3a36ecd2f967bd911c92c5
676,084
from datetime import datetime def ms_since_epoch(dt): """ Get the milliseconds since epoch until specific a date and time. Args: dt (datetime): date and time limit. Returns: int: number of milliseconds. """ return (dt - datetime(1970, 1, 1)).total_seconds() * 1000
3a7630c0930949f06573292729156c2e881107bd
676,086
def hasEnoughHarmonics(baseFrequency, harmonics): """ harmonics is an array of integers where each integer is represented as a string!!, e.g. "1" "3" "4" "5" NOTE: the standard says that at least 4 harmonics must be present for better spacial location of the sound it does not menti...
d0e5b191b34aedfb17510c2625533524a3200d95
676,087
import os def get_fetch_fout(filename): """Create a output file name where EFetch data will be stored.""" return ''.join([os.path.basename(os.path.splitext(filename)[0]), '.Entrez_downloads'])
7d8a6e0852013db13009b9caef72e850f7d17820
676,088
def prob15(size=20): """ Starting in the top left corner of a 2*2 grid, there are 6 routes (without backtracking) to the bottom right corner. How many routes are there through a 20*20 grid? """ a = 1 for i in range(1, size + 1): #print a a = a * (size + i) / i return a
73d088ee201991bf927b25e0be0d32f1d2ab17f3
676,089
import re def slugify(s): """ Simplifies ugly strings into something URL-friendly. >>> print slugify("[Some] _ Article's Title--") some-articles-title """ # "[Some] _ Article's Title--" # "[some] _ article's title--" s = s.lower() # "[some] _ article's_title--" # "[some]___ar...
fb403a0e8ff10e4c672f2fb3835da8b25877da46
676,090
def s2t_check(s2t_str): """ Example: tree_string = "(TOP (S (VP (VBP Do) (RB n't) (VP (VB be) (NP (JJ such) (DT a) (NN pessimist)) (, ,) (NP (NNP Mr.) (NNP Ambassador)))) (. .)))" _, tgt = tree_to_s2t(tree_string) print(s2t_check(tgt)) print(s2t_check(tgt + " /NP")) print...
a917e253069567f91380fb65427118e511401729
676,091
import os def blast(sample,db,output, identity=90, threads=1, mincov=0,dbtype='nucl'): """ Call blastn with params :param query_file (in fasta), db (blast indexed db), number of threads and identity :return: list BLASTFields objects """ #check db is indexed #dbfile=os.path.join(db_folder, ...
8b9a0e0f278d5adbf5bf8dc69671241bec5f356b
676,092
from typing import Optional def get_between(haystack: str, start_token: str, end_token: str) -> Optional[str]: """Returns the first instance of a string between start and tokens.""" start_idx = haystack.find(start_token) if start_idx == -1: return None start_idx += len(start_token) end_...
497a4f9abe7479fb4fa142fe8a76271578fd75b6
676,093
def get_side_menu_matrices(children): """Given a matrix structure defined in config.py, return stripped structure with only names""" def children_helper(matrix, path_prefix): children = matrix["subtypes"] return { "name": matrix["name"], "id": matrix["name"].spl...
3d6dbbe2ef0d108db0a18a81e6c2307f614f7c04
676,094
import functools def ensure_external_storage(fn): """Ensure management of external storage on methods which depend on it. :raises: ``errors.ExternalStorageNotInstalled`` :raises: ``errors.ExternalStorageDisabled`` """ # noqa @functools.wraps(fn) def wrapper(self, *args, **kwargs): ...
f73565ec061d3964535ee9e50919a26462134031
676,095
from typing import Optional def is_upper_case_name(name: Optional[str]) -> bool: """ Checks that attribute name has no upper-case letters. >>> is_upper_case_name('camelCase') True >>> is_upper_case_name('UPPER_CASE') True >>> is_upper_case_name('camel_Case') True >>> is_upper_c...
4735edf75dce024b881016a427f878f4dadde92d
676,096
import numpy def power_cheap(f1, f2=None, boxsize=1.0, average=True): """ stupid power spectrum calculator. f1 f2 must be density fields in configuration or fourier space. For convenience if f1 is strictly overdensity in fourier space, (zero mode is zero) the code still works. Does...
c1fd837277419fbc1bc369477b92611f7395d5c2
676,097
def serialize_table_umd(analysis, type): """ Convert the aggregate_values=false Hansen response into a table""" rows = [] for year in analysis.get('loss', None): rows.append({'year': year, 'loss': analysis.get('loss', None).get(year), 'gain': analysis.get('g...
a57a749e39ff5ebd696a8ac052100ba4186aa429
676,098
def gradient_descent(x0, grad, step_size, T): """run gradient descent for given gradient grad and step size for T steps""" x = x0 for t in range(T): grad_x = grad(x) x -= step_size * grad_x return x
c7b69ecc9291064835690b997477841414bfe6a9
676,099
def nm_to_n(s): """Get the nick part of a nickmask. (The source of an Event is a nickmask.) """ return s.split("!")[0]
19995784deef1d4cb31360e3bf3680286509e591
676,100
def get_lab_name(sen, labels): """ sen = list of numerical labels """ inv_l = {v: k for k, v in list(labels.items())} res = "" for i in sen: if i in inv_l: res = res + " " + inv_l[i] else: res = res + " *NEWLABEL" return res
99c64a8f2b2db51a08d7f5db6bb0652659e93dab
676,101
def reactionHasReactants(reaction, reactants): """ Return ``True`` if the given `reaction` has all of the specified `reactants` (and no others), or ``False if not. """ if len(reactants) == len(reaction.products) == 1: if reaction.products[0].isIsomorphic(reactants[0]): return Fa...
6e8f0da2f9756e96cd7f2f0b609b82d0c4772330
676,102
import linecache def get_title(notes_path, file_stem): """ Get the title by reading the second line of the .md file """ title = linecache.getline(notes_path + file_stem + '.md', 2) title = title.replace('\n', '') title = title.replace('title: ', '') return title
990047acbdcbf3e8d04c8167c59b985938829867
676,103
from typing import List from typing import Dict from typing import Any def sew_messages_and_reactions( messages: List[Dict[str, Any]], reactions: List[Dict[str, Any]] ) -> List[Dict[str, Any]]: """Given a iterable of messages and reactions stitch reactions into messages. """ # Add all messages wit...
01824e078fb7a44af6af80f49ff00b5ca5fcd3a6
676,104
def get_timing(line: str) -> str: """ Returns the stimulus timing from a line of text grabbed from a .vmrk file. """ return line.split(",")[2]
299d0e0cd9c84ee926c1a69828c4db966c09fff1
676,105
def empty_string_check(string, raise_exception=True): """ Simple check to see if the string provided by parameter string is empty. False indicates the string is NOT empty. Parameter raise_exception determines if a ValueError exception should be raised if the string is empty. If raise_exception is False and the str...
37b3ea789d31b9aec3c184e35026ad4b4f608d26
676,106
def get_public_key_from_x509cert_obj(x509cert) -> bytes: """ returns a RSA public key object from a x509 certificate object """ return x509cert.public_key()
896411f57781ae0b3537d2678345f0a69311b1e4
676,107
import os import string def getWinDrives(): """ Return list of detected drives """ assert os.name == 'nt' drives = [] bitmask = windll.kernel32.GetLogicalDrives() #@UndefinedVariable for letter in string.uppercase: if bitmask & 1: drives.append(letter) bitmask >>= 1 ...
0406ec175c5f498a1d6cdb580f5211469705cdf0
676,109
def home(): """ Welcome to the Station Climate Home Page """ return( f"""Available Routes:<br/><br/> /api/v1.0/precipitation<br/><br/> lists precipitation for last year of data<br/><br/> /api/v1.0/stations<br/><br/> lists all weather st...
85dd8f66272acbb7cd62839abe0c4f80ff769024
676,110
def getfieldnamesendswith(idfobject, endswith): """get the filednames for the idfobject based on endswith""" objls = idfobject.objls tmp = [name for name in objls if name.endswith(endswith)] if tmp == []: pass return [name for name in objls if name.endswith(endswith)]
09815199d2c4e0bfae3ee583d1b6d2391d4d6dc9
676,111