geraldmc

def omim_from_entrez():
    """Return a mapping from NCBI GeneIDs to OMIM IDs.
    Returns 17,108 entries from an original 26,371. 
    Sorted by key.
    """
    fp = './app/data/mim2gene.txt' # https://www.omim.org/static/omim/data/mim2gene.txt
    df = pd.read_csv(fp, skiprows=4, sep='\t',
                    usecols=['# MIM Number', 'Entrez Gene ID (NCBI)'])
    df.columns = ['omim', 'ncbi'] # rename columns
    df = df[np.isfinite(df['ncbi'])] # remove NaN's from ncbi

geraldmc

# Using GDAL to open a 4-band image created by Sequoia camera.

from osgeo import gdal  # Geospatial Data Abstraction Library
import numpy as np
import sys, os, re

def get_raster_bands(src_grayscale):
    """
    Each band is a 2d numpy array of real luminosity values.
    """

geraldmc

alias ipy="python -c 'import IPython; IPython.terminal.ipapp.launch_new_instance()'"

geraldmc

#!/usr/bin/env python

"""
=====================================
PEP 20 (The Zen of Python) by example
=====================================

Usage: %prog

:Author: Hunter Blanks, hblanks@artifex.org / hblanks@monetate.com

geraldmc

import requests

'''
Stand-alone script to search NYT articles, based on Evan Sherlock's original. Python3 enabled.

>> import nyt_article_search_api as nyt
>> api = nyt.articleAPI()
>> api/search()

'''

geraldmc

lshw -C memory 2>/dev/null | grep -Po ' +size: \K.*'

geraldmc

du -a /var | sort -n -r | head -n 10

geraldmc

library(igraph)
library(rgexf)
library(ggplot2)

# ggnet2 is available through the GGally package
# install.packages("GGally")
library(GGally)

# Following libraries will be required - used internally.
lapply(c("sna", "scales","intergraph", "network"),require, character.only=T)

geraldmc

import luigi

class FirstTask(luigi.Task):

    # The date when 'whatever' will be run.
    upload_date_param = luigi.DateParameter()

    def requires(self):
        """
        What needs to happen before FirstTask begins?

geraldmc

import luigi
from luigi.mock import MockTarget 

class FirstTask(luigi.Task):
    def output(self):
        return MockTarget("SimpleTask", 
            mirror_on_stderr=True)
 
    def run(self):
        _write = self.output().open('w')