programming-for-dummies

Bioinformatics Programming 631
Although a language like C/C++ runs on multiple platforms, porting a program
from Windows to Linux often requires rewriting to optimize the program for
each particular operating system. While figuring out C/C++ isn’t necessarily
hard, it’s not easy either.
A more appropriate programming language is a scripting language. Scripting languages,
such as Perl, run on almost every operating system, are easy to learn
and use, and include built-in commands for manipulating strings. Best of all,
scripting languages are specifically designed to work with existing programs
by feeding data to another program and retrieving the results back again.
Although Perl has become the unofficial standard programming language for
bioinformatics, biologists also rely on other programming languages because
many people feel that Perl is too confusing. Perl’s motto is “There’s more than
one way to do it” — you can perform the exact same action in Perl with
entirely different commands.
For example, to concatenate two strings, Perl offers two different methods.
The first is to smash two strings together, like this:
$DNA3 = “$DNA1$DNA2”;
The second way to concatenate the same two strings uses the dot operator,
like this:
$DNA3 = $DNA1 . $DNA2;
Book VII
Chapter 2
The second most popular language used in bioinformatics is Python. Python
offers identical features as Perl but many people feel that Python is a simpler
language to understand and use because its motto is, “There should be one —
and preferably only one — obvious way to do it.” To concatenate strings in
Python, you can use this command:
Bioinformatics
$DNA3 = $DNA1 + $DNA2
Another popular bioinformatics programming language is Java. Not only are
more programmers familiar with Java, but Java’s cross-platform capability also
allows it to create compiled programs for each operating system. In comparison,
both Perl and Python are interpreted languages — you must load the
source code of a Perl or Python program and run it through an interpreter first.
Java gives you the convenience of copying and running a compiled program
without the nuisance of running source code through an interpreter.
Despite the advantages of other programming languages, Perl is still the
language of bioinformatics. If you’re going to work in bioinformatics, first
learn Perl and then learn Python or Java.