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 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

# 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

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 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

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

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

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

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

# 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])