dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

from typing import Callable, Optional, Tuple, Iterable
from matplotlib.axes import SubplotBase
import seaborn as sns

def prettify_plot(plot_fn: Callable[[], SubplotBase],
        style :str='whitegrid',

dmyersturnbull

import numpy as np
def sliding_window(x: np.ndarray, n: int) -> np.ndarray:
    """Returns a sliding window of n elements from x.
    Raises a ValueError of n > len(x).
    """
    if n > len(x): raise ValueError("N must be less than the array length")
    # Courtesy of https://stackoverflow.com/questions/13728392/moving-average-or-running-mean
    return np.convolve(x, np.ones((n,)) / n, mode='valid')

dmyersturnbull

# This prints thisismypassword:
password = "thisismypassword"
function display_post(post_text)
    println("<p>$post_text</p>")
end
display_post("$pass" * "word")

# This doesn't when given $password (escaped) as an argument:
display_post(ARGS[1])

dmyersturnbull

from http_get import http_get # uses https://gist.github.com/dmyersturnbull/fade1a5901beeb1003680f8267454640
from typing import Mapping, Union, Iterable
import json

searchable_fields = {'alias_name', 'alias_symbol', 'ccds_id', 'ena', 'ensemble_gene_id',
                    'entrez_id', 'hgnc_id', 'locus_group', 'locus_type', 'mgd_id',
                    'name', 'prev_name', 'prev_symbol', 'refseq_accession', 'rgd_id',
                    'status', 'symbol', 'ucsc_id', 'uniprot_ids', 'vega_id'}

dmyersturnbull

# Douglas Myers-Turnbull wrote this while at UCSF. Because of this, the list of copyright owners is unknown and is not licensed (sorry!).

from dl_and_rezip import dl_and_rezip # see https://gist.github.com/dmyersturnbull/a6591676fc98da355c5250d48e26844e
from lines import lines
from typing import Mapping, Iterable, Optional, Iterator, Callable
import os
import warnings
import pandas as pd
import re

dmyersturnbull

from typing import Callable
import pandas as pd
from dl_and_rezip import dl_and_rezip # see https://gist.github.com/dmyersturnbull/a6591676fc98da355c5250d48e26844e


def _load(filter_fn: Callable[[pd.DataFrame], pd.DataFrame]=pd.DataFrame.dropna) -> pd.DataFrame:
    """Get a DataFrame of Human Protein Atlas tissue expression data, indexed by Gene name and with the 'Gene' and 'Reliability' columns dropped.
    The expression level ('Level') is replaced using this map: {'Not detected': 0, 'Low': 1, 'Medium': 2, 'High': 3}.
    Downloads the file from http://www.proteinatlas.org/download/normal_tissue.csv.zip and reloads from normal_tissue.csv.gz thereafter.

dmyersturnbull

import org.scalacheck.Gen
import org.scalatest.{PropSpec, Matchers}
import org.scalatest.prop.PropertyChecks

class MinimalScalaCheckExample extends PropSpec with PropertyChecks with Matchers {
	property("A string's length should be constant") {
		forAll { (s: String) =>
			s.length should equal(s.length)
		}
	}

dmyersturnbull

private implicit class Paddable(string: String) {
		/** Left-pad this string. */
		def ^(end: Int): String = " " * (end - string.length) + string
		/** Right-pad this string. */
		def $(end: Int): String = string + " " * (end - string.length)
	}

dmyersturnbull

using MAT
using Lumberjack

@doc """
Using MAT.jl, converts any MATLAB version >=5 .mat file to an HDF5-compatible MATLAB version 7 .mat file.
Warns if the file already exists.
""" ->
function convert_to_matlab7(input_file:: AbstractString, output_file:: AbstractString)
    if ispath(output_file)
        warn("File $output_file already exists")

dmyersturnbull

import gzip, io
from typing import Iterator

def lines(file_name: str, known_encoding='utf-8') -> Iterator[str]:
    """Lazily read a text file or gzipped text file, decode, and strip any newline character (\n or \r).
    If the file name ends with '.gz' or '.gzip', assumes the file is Gzipped.
    Arguments:
        known_encoding: Applied only when decoding gzip
    """
    if file_name.endswith('.gz') or file_name.endswith('.gzip'):