indraniel

# Based on reading : http://stackoverflow.com/questions/7936572/python-call-a-function-from-string-name
#                    http://stackoverflow.com/questions/3061/calling-a-function-of-a-module-from-a-string-with-the-functions-name-in-python
class Foo(object):
  
    def dynamic_call(self, attribute_name):
        method_name = 'calculate_' + attribute_name # e.g. given attribute name "baz" call method "calculate_baz" 
        func = getattr(self, method_name)           # find method that located within the class
        func()                                      # execute the method

indraniel

package main

// mentioned in bleve google group
// https://groups.google.com/forum/#!topic/bleve/-5Q6W3oBizY

import (
	"encoding/json"
	"fmt"
	"github.com/blevesearch/bleve"
	"github.com/blevesearch/bleve/document"

indraniel

package main

import (
	"archive/tar"
	"compress/gzip"
	"flag"
	"fmt"
	"io"
	"os"
)

indraniel

#!/bin/bash

# Usage:
#    bash b37-annotate-w-gnomAD.sh </path/to/input.vcf.gz> </path/to/output.vcf.gz>
#
# Note:
#    1. This script with create a "scratch" directory to hold intermediate file
#       states created during the annotation process.  The scratch directory will
#       be created next to the /path/to/outvcf.vcf.gz .  
#

indraniel

package main

import (
	"fmt"
	"github.com/syndtr/goleveldb/leveldb"
	"log"
)

func main() {
	db, err := leveldb.OpenFile("/tmp/foo.db", nil)

indraniel

This page is a curated collection of Jupyter/IPython notebooks that are notable for some reason. Feel free to add new content here, but please try to only include links to notebooks that include interesting visual or technical content; this should not simply be a dump of a Google search on every ipynb file out there.

Important contribution instructions: If you add new content, please ensure that for any notebook you link to, the link is to the rendered version using nbviewer, rather than the raw file. Simply paste the notebook URL in the nbviewer box and copy the resulting URL of the rendered version. This will make it much easier for visitors to be able to immediately access the new content.

Note that Matt Davis has conveniently written a set of bookmarklets and extensions to make it a one-click affair to load a Notebook URL into your browser of choice, directly opening into nbviewer.

indraniel

ssh-keygen -t ed25519 -C "information@food.com"
export GIT_SSH_COMMAND='ssh -i /Users/me/.ssh/id_ed25519_food_bitbucket -o IdentitiesOnly=yes'

indraniel

#!/opt/hall-lab/python-3.7.0/bin/python -u

import os, sys, time, datetime
import psutil

# add eagle to PATH
os.environ['PATH'] = os.pathsep.join(['/opt/hall-lab/eagle-2.4.1/bin', os.environ['PATH']])

def log(msg):
    timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")

indraniel

# http://flask.pocoo.org/snippets/88/

import os, sqlite3
from cPickle import loads, dumps
from time import sleep
try:
    from thread import get_ident
except ImportError:
    from dummy_thread import get_ident

indraniel

#!/usr/bin/env python

from __future__ import print_function
import ftplib, datetime, sys

# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

def log(msg):
    timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")
    print('[-- {} --] {}'.format(timestamp, msg), file=sys.stderr)