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Jack Simpson

Currently fascinated by energy markets and electrical engineering. In another life I was a beekeeper that did a PhD in computational biology writing image analysis software and using machine learning to quantify honeybee behaviour in the hive.

ContentProgrammingTips & Tutorials

Python os Module

by Jack Simpson
written by Jack Simpson

You can use the Python os module to send commands out to the operating system. Through os you can do anything from changing the current working directory through to listing the contents of a directory.

import os

# print the current working directory
print os.getcwd()
# change the working directory
os.chdir("..")
# create a new directory
os.mkdir("new_folder")
# list the contents of a directory
os.listdir("new_folder")
# remove directory
os.rmdir("new_folder")
# remove a file
os.remove("image.jpg")
# rename a file/directory and where it will go
os.rename("/data/jack", "/james")
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ContentLinuxTips & Tutorials

Useful Linux Commands

by Jack Simpson
written by Jack Simpson

Linux is an operating system – similar to Windows or Mac. It is freely available and very popular amongst researchers and programmers. Since many of the scripts you write will be run from the terminal, a list of popular Linux commands can be quite handy:

  • cd Used to change the directory (folder) which you have open. If I wanted to navigate to one of my directories I may write the command “cd /data/research/project”.
  • ls List the contents of a directory.
  • pwd Show the path to the current working directory.
  • mkdir This command followed by a name creates a directory.
  • rm Can be used to specify an empty directory or file you want to remove, for instance if you had a directory called ‘data’ you could delete it using “rm data”. If I wanted to delete all the files and directories in the directory “data”, I could use this command: “rm -rf data/*”.
  • tar –zxvf file.tar.gz Used to unzip a file.
  • chmod 777 filename.py Used to change the permissions on a file – this allows uses to read, write and execute this file.
  • sudo su – Enable root user privileges. You’ll be asked to input the root password if you issue this command.
  • cp firstname secondname Copy a file somewhere.
  • mv firstname secondname  Move a file and rename it.
  • ssh Log into another server using an SSH client through the terminal by inputting “ssh username@serveraddress”.
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ContentProgrammingTips & Tutorials

Parsing CSV Files in Python

by Jack Simpson
written by Jack Simpson

Almost anyone doing research at some point will have to input or extract data from an Excel spreadsheet. However, it is possible to export an Excel file as a .csv file (comma separated file) and then use Python to grab all the data instantly. The Python csv module makes all this incredibly simple:

import csv
column1 = []
column2 = []
column3 = []
openfile = csv.reader(open('data.csv'))
for row in openfile:
    first, second, third = row
    column1.append(first)
    column2.append(second)
    column3.append(third)

This script will open your .csv file, and then use the ‘.next()’ method to create an array of all the lines in your file, which you can parse through with the for loop.

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ContentProgramming

Logging into PuTTY with Perl

by Jack Simpson
written by Jack Simpson

When you use the SSH client PuTTY a lot, it can become quite tedious selecting your server and then writing in your username and password. That’s why I decided to write a short script in Perl to speed things up, and it looks like this:


use strict;
use warnings;
open my $copy, "| xclip";
print $copy Password";
close $copy;
my $external = `putty yourserver.com.au -l YourUsername -pw YourPassord`;

I’m copying my sudo password to the Linux application xclip so its ready in my clipboard, before opening PuTTY and automatically signing in. I then converted the script into an executable file using the instructions found here.

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ContentProgrammingTips & Tutorials

Running an R script through Python

by Jack Simpson
written by Jack Simpson

Before I made the switch to developing on a Linux machine, I noticed that the Python module for calling R (RPy2) seemed to be having some problems on Windows. This gave me an excuse to play around with writing my own Python script to create and run an R script. As you’ll see in the code below, I’ve used the subprocess module to execute the R script I created and then pipe the results back into the terminal.

import subprocess

# rscript is the content of the R file we'll create
rscript = '''#!/usr/bin/Rscript

cat('This is a simple program') # same as c()
NumOfIterations for (i in 1:NumOfIterations) { # 1:10 is range
cat(i, 'Hello world!')
cat(' ')
}
'''
r_file = open("example.r", "w")
r_file.write(rscript)
r_file.close()

r_file_name = "example.r"
ppath = r'C:Program FilesRR-2.15.2bini386Rscript.exe'
proc = subprocess.Popen("%s %s" % (ppath, r_file_name), stdout=subprocess.PIPE)
output = proc.stdout.read()
print output
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