krassowski

Work Product

Code written for project is available in repository on github: /reimandlab/Visualisation-Framework-for-Genome-Mutations.

For the day of writing evaluation I am the only author of code availalbe in the repository; as there might be other contributors in future: all commits prior to Aug 24, 2016 available here: /reimandlab/Visualisation-Framework-for-Genome-Mutations/commits/master?author=krassowski are my GSoC 2016 commits.

Collecting data was not the part of my work during GSoC 2016 - the data for application was provided by my Mentor and hence I mark explicitly that the content of the website/data directory is not part of my GSoC work (moreover it is not even code).

Deployment & reuse

krassowski

# 1. Create a directory with your name on your desktop
  mkdir ~/Desktop/Michal
# 2. Download a directory XYZ located in /home/login/somedir from login@host to your created directory
  cd ~/Desktop/Michal
  scp -r login@host:~/somedir/XYZ . # often you can skip '~/' after the colon - remote directories defaults to user's home
# 3. Merge files a.pdb with b.pdb, in this order, and save the result to c.pdb
  cd XYZ
  cat a.pdb b.pdb > c.pdb
# 4. Replace 'X' occurrences in lines 100-200 with 'Y' in the c.pdb file
  sed -ie '100,200s/X/Y/g' c.pdb  # the simplest way

krassowski

"""
A partial, lazy implementation of BCD (http://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-12-r271)
BiBS, Systems Biology workshops 2017
"""
from math import sqrt
from networkx import Graph, number_of_nodes, connected_component_subgraphs
from networkx.algorithms import edge_betweenness_centrality


def test_graph():

krassowski

#ifndef FORCEFIELD_HPP
#define FORCEFIELD_HPP
#include "vector.hpp"
#include "atom.hpp"
#include "system.hpp"

// I moved all code to one file for gist easier sharing ;)

// change to potential energy??
class ForceField {

krassowski

# The script is intended to demonstrate how to fetch data from UCSC easily
# (without mysql) in a way which will enable reproducibility of the download.

# It is NOT INTENDED as a generic tool for programmatic access to UCSC;
# Please respect UCSC request of avoiding issuing heavy queries as described in mysql usage manual;
# for more information on conditions of use, see: http://genome.ucsc.edu/goldenPath/help/mysql.html

# For advanced programmatic access you may be interested in setting you own local copy of UCSC database
# and using other, existing tools like: PyUCSC (see: https://pyucsc.readthedocs.io/en/latest)

krassowski

krassowski

from rpy2.robjects import r
from IPython import get_ipython

def rpy2_completer(ipython, event):
    query = event.line.strip().split()[-1]
    suggestions = []
    all_r_symbols = r('sapply(search(), ls)')
    for environment, symbols in all_r_symbols.items():
        for _, symbol in symbols.items():
            if symbol.startswith(query):

krassowski

from time import time
from IPython import get_ipython
from IPython.display import Audio, display

class Beeper:

    def __init__(self, threshold, **audio_kwargs):
        self.threshold = threshold
        self.start_time = None    # time in sec, or None
        self.audio = audio_kwargs

krassowski

# CC-BY-SA 4.0 Kevin (https://stackoverflow.com/a/41603739/6646912)
# https://creativecommons.org/licenses/by-sa/4.0/
from IPython.display import Audio, display

def play_sound(self, etype, value, tb, tb_offset=None):
    self.showtraceback((etype, value, tb), tb_offset=tb_offset)
    display(Audio(url='http://www.wav-sounds.com/movie/austinpowers.wav', autoplay=True))

get_ipython().set_custom_exc((ZeroDivisionError,), play_sound)

krassowski