Skip to content

Instantly share code, notes, and snippets.

View kantale's full-sized avatar

Alexandros Kanterakis kantale

View GitHub Profile
@kantale
kantale / gist:4656190
Last active December 11, 2015 20:38
Hello World
#This is a simple gist to test pypedia's "import gist" functionality
def Hello_world():
print "Hello World!"
@kantale
kantale / gist:4673621
Created January 30, 2013 14:28
import a non-existing module
import absentmodule
def abstent_module():
pass
@kantale
kantale / gist:4673642
Created January 30, 2013 14:31
Mandelbrot fractal
"""
This script uses the cplot function in mpmath to plot the Mandelbrot set.
By default, the fp context is used for speed. The mp context could be used
to improve accuracy at extremely high zoom levels.
"""
import mpmath
import cmath
import StringIO
{
"metadata": {
"name": "",
"signature": "sha256:d5382c1d8e4afa21ab324258164968c311a06f8bb46612ce600cbce5cbb39b75"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
@kantale
kantale / pypedia_example.ipynb
Created December 15, 2014 22:58
This is an example of hot to perform simple bioinformatics analysis with methods available on pypedia.com
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

Keybase proof

I hereby claim:

  • I am kantale on github.
  • I am kantale (https://keybase.io/kantale) on keybase.
  • I have a public key whose fingerprint is 3E1A 85D5 94C8 C30A 80A2 CE0B BD80 1DE0 A344 97B6

To claim this, I am signing this object:

@kantale
kantale / karyoplot.py
Created March 2, 2015 00:17
Plot chromosome Ideograms with karyotype with matplotlib
import os
import matplotlib
from matplotlib.patches import Circle, Wedge, Polygon, Rectangle
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
def karyoplot(karyo_filename, metadata={}, part=1):
'''
To create a karyo_filename go to: http://genome.ucsc.edu/cgi-bin/hgTables
@kantale
kantale / DeBoever_fig1_data.ipynb
Created September 26, 2015 17:57
IPython notebook that downloads the code and data needed to reproduce figure 1 for this publication: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004105
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

Introduction

This is the API documentation of the www.epga.gr service.

fetch_init_json

URL: http://www.epga.gr/explore/fetch_init_json/ Return type: JSON

Returns a JSON string with all available genes - drugs interactions. This is a small sample from the returned JSON file:

@kantale
kantale / example_tool.py
Last active March 8, 2016 04:47
How to setup galaxy with TORQUE in Amazon's cloud
#!/usr/bin/python
import sys
'''
Just a simple tool that adds the line number at
the end of each line
'''
with open(sys.argv[1]) as f_in, open(sys.argv[2], 'w') as f_out: