Final practical: How Many Articles Reference that they use R and/or Python?

Overview

Teaching: 30 min
Exercises: 60 min

Questions

• Can I write a command line Python progam using ArgParse?

Objectives

• Write a Python script that accepts arguments.

• Write a Python script opens a file and searches for words.

• Document your Python script using comments.

Final Practical

• This final practicle is going to combine all that you have learnt about Python into one command line program!
• The challenge is to write a command line Python progam using Argparse (under version control) that can:
  • Open a plain text file of a research article.
  • Search the article for references to R and/or Python.
    • bonus: search for the versions of R or Python.
  • Return the number of times the article refers to R and/or Python.
  • Choose whether or not to save the output and choose the output file name.

Example articles

Python PDF and XML

• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005871&type=printable
• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005871&type=manuscript

Python and R PDF and XML

• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005510&type=printable
• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005510&type=manuscript

R PDF and XML

• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004140&type=printable
• https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004140&type=manuscript

Need an Example of a Paper for without reference to either

Part 1 - Setup of Git Repository and Python Program

Open Git Bash and move to the directory where you want to work with your new Python project.
Now we need to initiate our new Git Repository so that we have our work under version control!

CHALLENGE: Initiate your git repository

Solution

git init python_prac

Next move to your new git folder python_prac and create our Python program by opening your chosen text
editor and saving it with an appropriate name.
e.g. using VIM in Git Bash. Write a comment # at the top of your program stating what it does and then save it.

vim ref_finder.py

Run git status to see if our new file is under version control.

git status

On branch master

No commits yet

Untracked files:
 (use "git add <file>..." to include in what will be committed)

       ref_finder.py

nothing added to commit but untracked files present (use "git add" to track)

CHALLENGE: Add and commit your python program so that is it under version control.

Solution

git add ref_finder.py
git commit -m "inital commit"

Now we are ready to start coding!!

Part 2 - Structure of Python Program

CHALLENGE: How do we Start? Write down in words what you want your program to do.

Hint

1. Read in the words in a chosen text document (text file - XML) line-by-line.
2. Search the document for the words “R” and/or “Python”.
3. Count the number of times the words “R” and/or “Python”.
4. Print out the result.
5. Save the result to a text document.

CHALLENGE: Open a Jupyter Notebook and write code to read a text file line by line and print each line.

Solution

file = 'absolute file location'
with open(file, "r") as f:
   for line in f:
       print(line)

CHALLENGE: Copy your Jupyter Notebook script into a new panel and integrate a string search for ‘Python’ and print the number of counts.

Solution

file = 'absolute file location'
with open(file, "r") as f:
   for line in f:
       if line.string("Python") == True:
           count += 1
       print("Python was found", count, "times")

CHALLENGE: In a new panel in your Jupyter Notebook, turn your script into a reusable function.

Solution

def ref_finder(file_location):

   file = file_location
   with open(file, "r") as f:
       for line in f:
           if line.find("Python") == True:
               count += 1
           print("Python was found", count, "times")

CHALLENGE: Copy your function into your ref_finder.py program and integrate Argparse so that your program can accept any file from the command line.

Solution

import argparse

def ref_finder(file_location):

   file = file_location
   with open(file, "r") as f:
       for line in f:
           if line.find("Python") == True:
               count += 1
           print("Python was found", count, "times")

parser = argparse.ArgumentParser()
parser.add_argument("file_location")
args = parser.parse_args()
ref_finder(args.file_location)

CHALLENGE: Update your ref_finder.py program to include optional arguments so you can search for references to ‘R’ or ‘Python.

Solution

import argparse

def ref_finder(file_location, language):

   file = file_location
   string = language
   with open(file, "r") as f:
       for line in f:
           if line.find(string) == True:
               count += 1
           print(string, "was found", count, "times")

parser = argparse.ArgumentParser()
parser.add_argument("file_location")
parser.add_argument("language")
args = parser.parse_args()
ref_finder(args.file_location, args.language)

CHALLENGE: Update your ref_finder.py program so that it can search for both ‘R’ and ‘Python’ as an optional argument, printing the counts for both.

Solution

import argparse

def ref_finder(file_location, language, count_both):

   file = file_location
   if both == True:
       string1 = 'R'
       string2 = 'Python'
       with open(file, "r") as f:
       for line in f:
           if line.find(string1) == True:
               R_count += 1
           if line.find(string2) == True:
               Py_count += 1
           print(string1, "was found", R_count, "times")
           print(string2, "was found", Py_count, "times")
   else:
       string = language
       with open(file, "r") as f:
           for line in f:
               if line.find(string) == True:
                   count += 1
               print("string", "was found", count, "times")

parser = argparse.ArgumentParser()
parser.add_argument("file_location")
parser.add_argument("language")
parser.add_argument("-b", "--count_both", default = False)
args = parser.parse_args()
ref_finder(args.file_location, args.language, args.count_both)

Key Points

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