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 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

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

# 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

# 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

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
}