Zientzilaria

Covering the bioinformatics niche and much more

Importing and Regular Expressions

| Comments

Tisdall’s book on Perl introduces next the ability to transcripts DNA sequences into RNA. In order to do that we need to check a different aspect of programming: regular expressions (or regex). Regular expressions is a pattern/string expression that works matching/describing/filtering other strings. Let’s say you want to examine or extract all vowels contained in one phrase, one page, one word. Another example would be to remove all html tags from a downloaded webpage. As HTML tags are encapsulated between < and > signs we can create a regex that will search for any characters in between the signs and remove (parse) them from our page. We will deal very briefly with regex, and if you are interested in learning more about it you can search for countless references on the internet (such as this one).

In order to use regular expression in Python we need to check another concept present in the language: importing modules. Python core functionality provides most of the usual operations and also comes with a built-in library of functions that “access to operations that are not part of the core of the language but are nevertheless built in”. One of this operations is the ability to interpret regular expression that in Python is located in the re module. Apart from the language core, built in modules, Python can be further extended by using third-party modules imported into the language. Anyone can create a module and distribute to every Python user and programmer. So, in order to have regex capabilities we literally have to import the regex module. We do that by entering the line:

1
import re

Python’s code style guide suggests that import statements should be on separate lines

1
import sys import re ...

and to be put on the top of the file (usually below the line that tells your OS to use Python’s interpreter on the script). So the first two lines of our new script would be

1
2
\#! /usr/bin/env
python import re

Now that we have the ability to use regex,we need to create one expression that will transcribe our DNA sequences into RNA.