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@kantale
kantale / gist:4656190
Last active Dec 11, 2015
Hello World
View gist:4656190
#This is a simple gist to test pypedia's "import gist" functionality
def Hello_world():
print "Hello World!"
@kantale
kantale / gist:4673621
Created Jan 30, 2013
import a non-existing module
View gist:4673621
import absentmodule
def abstent_module():
pass
@kantale
kantale / gist:4673642
Created Jan 30, 2013
Mandelbrot fractal
View gist:4673642
"""
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
View gist:dda2a1bf861bd9bef91e
{
"metadata": {
"name": "",
"signature": "sha256:d5382c1d8e4afa21ab324258164968c311a06f8bb46612ce600cbce5cbb39b75"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
@kantale
kantale / pypedia_example.ipynb
Created Dec 15, 2014
This is an example of hot to perform simple bioinformatics analysis with methods available on pypedia.com
View pypedia_example.ipynb
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View keybase.md

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 Mar 2, 2015
Plot chromosome Ideograms with karyotype with matplotlib
View karyoplot.py
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 Sep 26, 2015
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
View DeBoever_fig1_data.ipynb
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View EPGA_API.md

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 Mar 8, 2016
How to setup galaxy with TORQUE in Amazon's cloud
View example_tool.py
#!/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:
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