content
stringlengths
42
6.51k
def get_circular( locus_text: str) -> bool: """ Args: locus_text: The LOCUS (i.e. header section) of genbank file """ line1 = locus_text[:locus_text.find('\n')] if ' circular ' in line1: return True return False
def transform_color(color1, color2, skipR=1, skipG=1, skipB=1): """ transform_color(color1, color2, skipR=1, skipG=1, skipB=1) This function takes 2 color1 and color2 RGB color arguments, and then returns a list of colors in-between the color1 and color2 eg- tj.transform_color([0,0,0],[10,10,20]) returns a list:...
def parse_style(style_string: str) -> dict: """[summary] Args: style_string (str): [description] Returns: dict: [description] """ return {kv.split(':')[0]:int(kv.split(':')[1]) if kv.split(':')[1].isdigit() else kv.split(':')[1] for kv in style_string.split(';')}
def expand_locations(ctx, values, targets = []): """Expands the `$(location)` placeholders in each of the given values. Args: ctx: The rule context. values: A list of strings, which may contain `$(location)` placeholders. targets: A list of additional targets (other than the calling rul...
def not_(x): """Support `not x` syntax""" if bool(x): return False return True
def get_chromosome_number(chrom: str) -> int: """ Get chromosome number (index) of the supplied chromosome: '1' -> 1, chr1 -> 1, returns -1 when not available, chrM -> -1 """ try: return int(chrom.replace('chr','')) except Exception as e: return -1
def _get_time_split(timing_line): """Extracts timing information from a boost-formatted timestamp, i.e.: <timestamp> GeometricCalibration.cpp:<line_number> Aggregate timing: <wall>s wall, <user>s user + <system>s system = <cpu>s CPU (<pct>%) Args: timing_line (str): Line of the above format. ...
def groupBy(keyFn, row_data): """Group rows in row_data by the result of keyFn. Arguments: keyFn -- A function that returns the cell data of the column to group by. Needs to be tailored to the structure of row_data. row_data -- A table organized as a list of row data structures. Retur...
def get_prob(date): """get the file name of the probability""" date = str(date) ret = date + 'prob.csv' return ret
def connect_(pairs, n=1): """connect_ Connects two adjacent clusters if their distance is <= n :param pairs: Clusters of iterateables e.g., [(1,5),(7,10)] :param n: distance between two clusters """ if len(pairs) == 0: return [] start_, end_ = pairs[0] new_pairs = [] for i,...
def _hashable_bytes(data): """ Coerce strings to hashable bytes. """ if isinstance(data, bytes): return data elif isinstance(data, str): return data.encode('ascii') # Fail on anything non-ASCII. else: raise TypeError(data)
def parse_directions(input_directions): """Parse input_directions for single tile from str to list of str.""" directions = [] index = 0 while index != len(input_directions): left = input_directions[index:] if left.startswith('s') or left.startswith('n'): directions.append(lef...
def header_from_line(line): """ Parse a tsv header :param line: the header text :return: (column_names list, column_indices dict) """ if len(line) == 0: return [], {} column_names = line.rstrip("\n").split("\t") column_indices = dict([(name, index) for index, name in enumerate(column_names)]) return colum...
def sortable_label(label, separator='-'): """ Create a sortable tuple out of a label. Converts a dashed label into a tuple based on the following rules: - If a segment is numeric, it will get three leading zero places - If a segment is alphabetic and is already uppercase, it is retur...
def wrap_text(text, font, width): # ColdrickSotK # https://github.com/ColdrickSotK/yamlui/blob/master/yamlui/util.py#L82-L143 """Wrap text to fit inside a given width when rendered. :param text: The text to be wrapped. :param font: The font the text will be rendered in. :param width: The width t...
def is_pangram(s): """Return True if str `s` is a pangram, False otherwise >>> is_pangram("The quick brown fox jumped over the lazy dog.') True >>> is_pangram("The slow brown fox jumped over the lazy dog.') False """ return len(set([c for c in s.lower() if 'a' <= c <= 'z'])) == 26
def reverse_linked_list_recursive(head): """Excercise 1.3.30 Recursively reverese a linked list.""" if head is None: return if head.next is None: return head second = head.next rest = reverse_linked_list_recursive(second) second.next = head head.next = None return rest
def round_nearest(value, multiple_of): """round to `multiple_of` value. based on: https://stackoverflow.com/a/28425782/574981 """ return round(value / multiple_of) * multiple_of
def zero2minimum(single_data): """change the value which is zero into 0.0000001 :param single_data: data point :return: data which may be 0.0000001 """ single_data = 0.0000001 if single_data == 0 else single_data return single_data
def trimText(message): """ This functions cleans the string It removes all the characters without A-Z, a-z :param message: The string which I want to trim :return: returns a string """ trimmed_text = [] for i in range(len(message)): if 'A' <= message[i] <= 'Z' or 'a' <= message[i...
def _get_gl_version(_lib): """Helper to get the GL version string""" try: return _lib.glGetString(7938).decode('utf-8') except Exception: return 'unknown'
def program_counter(c): """program counter""" v = "c.pc" return v
def divide_dict(a_dict, divide_func): """Divide a dict like object into two parts. - a_dict: dict like object - divide_func: the divide function to return True/False Return two parts of the dict. Example: divide({'a': 1, 'b': 2}, lambda k, v: v > 1) -> {'b': 2}, {'a': 1} """ suit,...
def is_good_candidate(input_string, guess_word): """ input_string: string, the user input to be spellchecked guess_word: string, the word from the wordlist to be checked for candidacy returns: bool, True if the guess is of good length and the beginnings and endings of both of the strings match up co...
def check_for_repeats(string): """ Returns a tuple of booleans, the first if duplicates exist, the second if triples do. """ double = False triple = False counts = {} for c in sorted(string): if c in counts: counts[c] += 1 else: counts[c] ...
def normalize(value: float, min_value: float, max_value: float) -> float: """Normalize value to range [0..1]""" if min_value == max_value: return 0 if not min_value <= value <= max_value: raise ValueError(f"Value {value} is not in range [{min_value}; {max_value}]") return (value - min_va...
def get_adjacents(row, col, max_row, max_col): """ Obtains the directions of the adjacent spaces """ result = [] up_row = row - 1 left_col = col - 1 down_row = row + 1 right_col = col + 1 if up_row >= 0: result.append((up_row, col)) if left_col >= 0: result.append...
def get_disabled_vhost_path(version, domain): """ Get the path for a disabled PHP vhost file regardless of wether or not it exists. Args: version - The PHP version used in the file path domain - The domain used in the file path """ return '/opt/php-' + version + '/etc/php-fpm.d/' + ...
def _add_algorithm_defaults(algorithm): """Central location specifying defaults for algorithm inputs. Converts allowed multiple inputs into lists if specified as a single item. """ defaults = {"archive": [], "min_allele_fraction": 10.0, "tools_off": []} convert_to_li...
def compute_cycle_length_with_denom(denom): """ Compute the decimal cycle length for unit fraction 1/denom (where denom>1) e.g. 1/6 has decimal representation 0.1(6) so cycle length is 1, etc """ digit_pos = 0 # Remaining fraction after subtracting away portions of earlier decimal digits fr...
def get_contiguous_pairs(sequence: list, pair_size: int) -> list: """" DOCTEST >>> get_contiguous_pairs(sequence=[1, 2, 3, 4], pair_size=2) [[1, 2], [2, 3], [3, 4]] >>> get_contiguous_pairs(sequence=[1, 2, 3, 4], pair_size=3) [[1, 2, 3], [2, 3, 4]] """ return [sequence[i:i + pair_size] ...
def coulomb_force(q1, q2, r): """ Calculates the force between two point charges. Applying coulombs law of F = k * q_1 * q_2 / r ** 2 to find the force of attraction/repulsion between two charges based on their distance from each other. :param q1: Scalar: Charge given in Coulombs :param q2: Sc...
def format_tuple(tup, join_char="."): """Formats a tuple of Version numbers for printing. Example: (4, 2, 0) turns into 4.2.0 Args: tup (tuple): Version as tuple. join_char (char): Character by which numbers are joined (default: ".") Returns: str: Joined version number. ...
def rk4(x, v, t, h, deriv): """ Core Rk4 algo for calculating one step ahead. This version is limited to 2nd order eq's of the type dx^2/dt^2 + p(t,x,v)*dx/dt + q(t,x,v)*x = r(t,x,v) Input: - x: x (t) - v: v (t) - t: Initial time (t_n) - h: Stepsize (t_{n+1} = t_...
def c3_merge(bases): """ Merge together the list of base classes into the mro that will be created using the C3 linearisation algorithm """ # Protect against empty base class lists (although this should never happens # because everyone derives from object *right*?) if not bases: retu...
def fetchPID( pid ): """ Read in the HST visit status page for the given program ID. """ import sys try: from bs4 import BeautifulSoup as bs except ImportError : print("Error: hstMonitor requires BeautifulSoup4.") print(" http://www.crummy.com/software/BeautifulSoup")...
def process(proc_data): """ Final processing to conform to the schema. Parameters: proc_data: (dictionary) raw structured data to process Returns: List of dictionaries. Each dictionary represents a row in the csv file: [ { csv file converted to a Dict...
def _stringify_na_values(na_values): """ return a stringified and numeric for these values """ result = [] for x in na_values: result.append(str(x)) result.append(x) try: v = float(x) # we are like 999 here if v == int(v): v = int(...
def rivers_with_station(stations): """Returns a list containing the names of all the rivers that have at least one of the stations provided as input""" # Add the rivers of all stations to a set so they are not repeated. rivers = set() for station in stations: rivers.add(station.river) # Re...
def distance_to_buckets(d): """converts distance to one-hot vector""" ohe = [0] * 10 if d == 0: ohe[0] = 1 elif d == 1: ohe[1] = 1 elif d == 2: ohe[2] = 1 elif d == 3: ohe[3] = 1 elif d == 4: ohe[4] = 1 elif 5 <= d < 8: ohe[5] = 1 elif ...
def extract_keys(inp_dict, keys): """ Return dictionary witxh selected keys :param inp_dict: dictionary :param keys: list or string :return: dictionary """ if not isinstance(keys, list): keys = [keys] return {your_key: inp_dict[your_key] for your_key in keys}
def get_mips_per_model(models_and_mips, cmip6_model): """ Identifies the mips for that specific model input. :param models_and_mips: :param cmip6_model: :return: mips """ for model, mips in models_and_mips.items(): if model == cmip6_model: return mips raise Excepti...
def pair_gcd(a,b): """Return greatest common divisor using Euclid's Algorithm.""" while b: a, b = b, a % b return a
def get_task_name(request, default): """Use 'shadow' in request for the task name if applicable.""" # request.shadow could be None or an empty string. # If so, we should use default. return getattr(request, 'shadow', None) or default
def split_network_line(line): """Parses line of /proc/virtual/<xid>/cacct for network usage. The cacct file has a header followed by usage counts for multiple protocols. Header (provided for context): Type recv #/bytes send #/bytes fail #/bytes Each protocol's usage counts are formatte...
def str_to_positive_int(text): """ Convert a string representation back to PositiveInt. """ if text.strip(): val = int(text) if val >= 0.: return int(text) else: raise ValueError("Value should be positive.") else: return 0
def significant_magnitude(num): """ Return an integer of -1, 0, or 1 based on magnitude with an arbitrary significance of 0.07 """ if -0.08 < num < 0.08: return False return True
def get_public_STATE_transitions(self, field="state"): """ Returns the transitions which are meant to be seen by the customer. The admin on the other hand should be able to see everything. :param str field: the name of the :class:`~django_states.fields.StateField` """ if getattr(self, "_%s_log_...
def join_deps(deps, commasep=True): """ Take the result from explode_dep_versions and generate a dependency string """ result = [] for dep in deps: if deps[dep]: if isinstance(deps[dep], list): for v in deps[dep]: result.append(dep + " (" + v +...
def is_overlapped(end1, start2): """Returns True if segments are overlapping. Arguments --------- end1 : float End time of the first segment. start2 : float Start time of the second segment. Returns ------- overlapped : bool True of segments overlapped else Fals...
def search4vowels(phrase: str) -> set: """Returns the set of vowels found in 'phrase'.""" return set('aeiou').intersection(set(phrase))
def excel_column_name(n): """Number to Excel-style column name, e.g., 1 = A, 26 = Z, 27 = AA, 703 = AAA.""" name = '' while n > 0: n, r = divmod (n - 1, 26) name = chr(r + ord('A')) + name return name
def remove_index(a, index): """Remove element at index of a sequence and return it as a list""" a = list(a) a.pop(index) return a
def _CompareLocaleLists(list_a, list_expected, list_name): """Compare two lists of locale names. Print errors if they differ. Args: list_a: First list of locales. list_expected: Second list of locales, as expected. list_name: Name of list printed in error messages. Returns: On success, return Fal...
def hex_to_rgb(hex_color): """ Converts a 6 digit hex number to RGB. @param: hex_color - A 6 digit string with values in the range [a-fA-F0-9]. @return: a tuple containing 3 integers. """ if not isinstance(hex_color, str): raise TypeError("'hex_color' must be of type 'str'.") if le...
def factorize(n): """Returns list of prime factors of positive integer n.""" i = 2 factors = [] while True: q, r = divmod(n, i) if r: i += 1 if i > n: return factors else: factors.append(i) if q < i: ...
def date_span_intersection(date_span_1, date_span_2): """Return a tuple of dates representing the overlap between `date_span_1` and `date_span_2`. If the date spans do not overlap, return `None`. """ intersection_first_date = max(date_span_1[0], date_span_2[0]) intersection_second_date = min(date_s...
def lr_schedule(epoch: int, lr: float): """ Scheduler function for keras callback. :param epoch: Epoch number. :param lr: Initial learning rate. :return: Updated LR. """ if epoch < 40: lr_ = lr elif epoch < 60: lr_ = lr / 3 elif epoch < 70: lr_ = lr / 5 el...
def average(a, b): """ :param a: int, sum of total value :param b: int, the amount of temp information :return: a / b """ avg = a / b return avg
def validate_target_port(value): """Raise exception if target port fails to match length constraint.""" if value and value["Port"] > 65535: return "have value less than or equal to 65535" return ""
def s2n(s): """ s2n(string) -> int String to Number """ return int(s.encode('hex'),16) if len(s) else 0
def getScriptName(programName): """ Splits a given string suspected to be a file name and returns the prefix with out the file extension. Args: programName: String file name candidate. Returns: prefix of file. """ # Script name scriptName = programName.split('.')[0].upper()...
def dict_access(d, key): """Access a key in a dict using . notation (key.subkey1.subkey2...subkeyn) returns None if the key path does not exist in the object""" current = d for subkey in key.split("."): try: current = current[subkey] except KeyError: return None ...
def findXDeltaFromDirection(direction): """ Returns delta X for jumping, when given a direction value """ if direction in (2, 4): return 2 elif direction in (6, 8): return -2 else: error_template = "Unexpected direction value of: {0}" raise ValueError(error_template.forma...
def single_line(value): """Returns the given string joined to a single line and trimmed.""" return " ".join(filter(None, map(str.strip, value.splitlines())))
def decompose_code(code): """ Decomposes a MARC "code" into tag, ind1, ind2, subcode """ code = "%-6s" % code ind1 = code[3:4] if ind1 == " ": ind1 = "_" ind2 = code[4:5] if ind2 == " ": ind2 = "_" subcode = code[5:6] if subcode == " ": subcode = None return (code[0:3], ind1,...
def get_sh_resource_type(iot_finding): """Return ASFF Resource type based on IoT Device Defender finding""" return "AwsIamRole" if iot_finding['nonCompliantResource']['resourceType'] == "IAM_ROLE" else "Other"
def camel_to_snake(word: str, depublicize: bool = False): """Convert came case to snake case.""" word = "".join(["_" + i.lower() if i.isupper() else i for i in word]) if not depublicize: word = word.lstrip("_") return word
def rankine2kelvin(K): """ Convert Rankine Temperature to Kelvin :param K: Temperature in K Kelvin :return: Temperature in R Rankine """ return 5.0 / 9.0 * K
def getBucketName(year, month, day, radar): """ Get the name of a specific bucket where radar data is stored. Args: year: Year as an integer. month: Month as an integer. day: Day as an integer. radar: The 4 letter name of the radar, a string. Returns: The bucket nam...
def calc_results_progress( number_of_users: int, number_of_users_required: int, cum_number_of_users: int, number_of_tasks: int, number_of_results: int, ) -> int: """ for each project the progress is calculated not all results are considered when calculating the progress if the requir...
def cube(number): """ Returns True if number is cube """ if number == 1: return True root = round(number ** (1. / 3)) return root**3 == number
def get_next_run_id(root, scheme_entry): """Cycles through a root object to get the next unique run_id string for a new measurement""" i = 1 while True: run_id = 'run_' + str(i) try: existing_weighing = root['Circular Weighings'][scheme_entry]['measurement_' + run_id] ...
def cmd_if(ctx, cond, true_block, false_block=None): """ It returns true block if condition occur """ return true_block if cond else false_block or []
def CheckForExistence(requested_data, available_data): """Determine whether the requested data exists. Args: requested_data: The specific data being requested. available_data: The full set of available data to tell whether it is just the requested data that does not exist, or no data exists at all....
def raise_to_list(input): """ This will take an input and raise it to a List (if applicable). It will preserve None values as None. Parameters ---------- input : object The object to raise to a list. Returns ------- list The object as a list, or None. """ if inp...
def list_union(start_list, then_include) -> None: """ This method ensures an output that includes everything from both lists """ if type(then_include) is str: if then_include not in start_list: start_list.append(then_include) elif type(then_include) is list: for item in t...
def compress_data(data): """Remove all keys from ``data`` that refer to themselves:: >>> data = {'a': 'a', 'b': 'c'} >>> compress_data(data) {'b': 'c'} """ compressed = {} for k, v in data.items(): if not k == v: compressed[k] = v r...
def byte_to_signed_int(x): """ Returns a signed integer from the byte :param x: Byte """ if (x & 0x80) >> 7 == 1: return -((x-1) ^ 0xff) else: return x
def format72(value): """ Adapt string to fit on a 72 line @param value (string) The string to adapt @param (string) The updated string """ val72 = '' for i in range(int(len(value)/71)+1): val72 = val72 + (value+71*' ')[71*i:71*i+71] + '\n' return val72.rstrip()
def replace_variables_in_text(function_with_text, variables): """ Perform variable replacement in text """ return function_with_text.__doc__.format(**variables)
def cleanup_salary(row): """to clean salary to replace $ sign """ salary = row["Salary"].replace("$", "") salary = float(salary) return salary
def to_reduced_row_echelon_form(matrix): """ This method computes the reduced row echelon form (a.k.a. row canonical form) of a matrix. The code is taken from https://rosettacode.org/wiki/Reduced_row_echelon_form#Python and edited with minor changes. :param matrix matrix: matrix to be ...
def indent(text, numtabs=1, spacespertab=4, tab=None): """ Indents a given multiline string. By default, indentation is done using spaces rather than tab characters. To use tab characters, specify the tab character explictly, e.g.:: indent(text, tab='\t') Note that in this...
def remove_item(thislist, item): """ Remove item from list without complaining if absent @param thislist : list of items @param item : item which may or may not be in the list @return: reduced list """ try: thislist.remove(item) except ValueError: pass return thislist
def readgenefile(genefile): """ Get the gene list """ success = False try: with open(str(genefile), 'r') as f: lines = [line.rstrip('\n').split(',') for line in f] genes = [line[0] for line in lines] linkers = [line[1:] for line in lines] success = Tru...
def is_2numbers(astring): """ (str) -> Boolean returns True if astring has at least two numbers. else return False. >>> is_2numbers('CIS122') True >>> is_2numbers('Ducks') False >>> is_2numbers('ABC-1') False """ digits_ctr = 0 for c in astring: if c.is...
def left_remove(text, to_remove): """ Removes a part of a string, if it starts with it. Similar to str.lstrip, see note below on right_remove """ if text.startswith(to_remove): return text.replace(to_remove, '', 1) else: return text
def get_engagement_rate_max(selectpicker_id: str) -> int: """ Max-Delegate-target of get_engagement_rates_min_max (dac-pattern) :param selectpicker_id: :return: int -> max-value of engagement-rate """ max_values = { "1": 1, "2": 2, "3": 3, "4": 4, "5": 5,...
def format_author_ed(citation_elements): """Standardise to (ed.) and (eds.) e.g. Remove extra space in (ed. ) """ for el in citation_elements: if el['type'] == 'AUTH': el['auth_txt'] = el['auth_txt'].replace('(ed. )', '(ed.)') el['auth_txt'] = el['auth_txt'].replace('(ed...
def make_dict_from_tree(element_tree): """Traverse the given XML element tree to convert it into a dictionary. :param element_tree: An XML element tree :type element_tree: xml.etree.ElementTree :rtype: dict """ def internal_iter(tree, accum): """Recursively iterate through the elements...
def str2int(val): """ Converts a decimal or hex string into an int. Also accepts an int and returns it unchanged. """ if type(val) is int: return int(val) if len(val) < 3: return int(val, 10) if val[:2] == '0x': return int(val, 16) return int(val, 10)
def assign_rank_group(atom_num, assign, rank, rank_num): """ | **Description:** Assign rank to each group **Input:** - atom_num: Atom respectively which we are producing the rank from - assign: Group of molecules grouped on clusters dependiong on the ligand connectivity - rank: list o...
def sanitise(dic): """Adds underscores to keys in dictionary""" new_dic = dict() for key, value in dic.items(): new_dic["_{}".format(key)] = value return new_dic
def mutual_information_calc(response_entropy, conditional_entropy): """ Calculate Mutual information. :param response_entropy: response entropy :type response_entropy: float :param conditional_entropy: conditional entropy :type conditional_entropy: float :return: mutual information as float...
def is_full_connected (v: int, r: int) -> bool: """ This function checks if graph is full connected. :param v: number of nodes graph has :param r: number of edges graph has :return: True if all nodes are connected, otherwise False :example: >>> is_full_connected(0, 1) False >>> is...
def _create_tree_from_edges(edges): """ Examples -------- >>> from pprint import pprint >>> pprint(_create_tree_from_edges([[1,2],[0,1],[2,3],[8,9],[0,3]])) {0: [1, 3], 1: [2, 0], 2: [1, 3], 3: [2, 0], 8: [9], 9: [8]} Parameters ---------- edges : list of pairs """ tree = ...
def _is_spec_data(spec, spectype): """ Checks to see if the spec is data only Args: spec: to check spectype: if any available Returns: true if only data, false if it is a spec """ if spec == 'nested' or spectype == 'nested': return False # if it is not a dic...
def _prepare_toc(toc): """Prepare the TOC for processing.""" # Un-nest the TOC so it's a flat list new_toc = [] for chapter in toc: sections = chapter.get('sections', []) new_toc.append(chapter) for section in sections: subsections = section.get('subsections', []) ...
def smart_rename(dic): """ assign MW in MDa or KDa depending on the string """ for k in dic: if len(dic[k].split(".")[0]) > 6: dic[k] = str(round(float(dic[k]) / 1000000, 2)) + " MDa" else: dic[k] = str(round(float(dic[k]) / 1000, 2)) + " KDa" return dic