dmyersturnbull

case class UnorderedPair[A](a: A, b: A) {
	override def equals(o: Any) = o match {
		case that: UnorderedPair[A] => that.a == a && that.b == b || that.a == b && that.b == a
		case _ => false
	}
	override def hashCode = a.hashCode * b.hashCode // commutative and unique
}

dmyersturnbull

# Requires https://gist.github.com/dmyersturnbull/c0717406eb46158401a9:
from silenced import silenced

import re
import uniprot # from https://github.com/boscoh/uniprot
import pandas as pd
import contextlib
import sys
from io import StringIO
from typing import Iterable, Union, Mapping

dmyersturnbull

# Requires https://gist.github.com/dmyersturnbull/efe32052bf4cf06df915

import pandas as pd
from typing import Iterable, Union, Mapping
from goatools import obo_parser # uses https://github.com/tanghaibao/goatools
from goatools.obo_parser import GOTerm # NOT the same as FlatGoTerm, which has no knowledge of hierarchy


if not os.path.exists('gene_ontology.1_2.obo'):
    import wget

dmyersturnbull

import contextlib
import sys
from io import StringIO

@contextlib.contextmanager
def silenced(no_stdout=True, no_stderr=True):
    """
    Suppresses output to stdout and/or stderr.
    Always resets stdout and stderr, even on an exception.
    Usage:

dmyersturnbull

import warnings
import numpy as np
from typing import Iterable, Mapping, Callable, Any, Tuple
def converge(sampler: Callable[[None], Iterable[float]],
                             statistic:Callable[[np.ndarray], float]=np.mean,
                             ε:float=0.01, min_iters:int=3, max_iters:int=50,
                             noter:Callable[[int, float, float, Iterable[float]], Any]=lambda i, estimate, delta, samples: print('Iteration {}: {:.3f}, δ=={:.3f}'.format(i, estimate, delta))
            ) -> Tuple[float, Iterable[float]]:
    """Repeatedly sample something until the mean (or other statistic) converges to within ε.
    

dmyersturnbull

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

import chemspipy
from chemspipy import ChemSpider
import warnings
from typing import Iterable, Mapping, Optional
import warnings
import time

# use your API key for fetching from ChemSpider

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'):

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

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

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)
		}
	}