2.2 Perl's Benefits

The following sections illustrate some of Perl's strong points.

2.2.1 Ease of Programming

Computer languages differ in which things they make easy. By "easy" I mean easy for a programmer to program. Perl has certain features that simplifies several common bioinformatics tasks. It can deal with information in ASCII text files or flat files, which are exactly the kinds of files in which much important biological data appears, in the GenBank and PDB databases, among others. (See the discussion of ASCII in Chapter 4; Genbank and PDB are the subjects in Chapter 10 and Chapter 11.) Perl makes it easy to process and manipulate long sequences such as DNA and proteins. Perl makes it convenient to write a program that controls one or more other programs. As a final example, Perl is used to put biology research labs, and their results, on their own dynamic web sites. Perl does all this and more.

Although Perl is a language that's remarkably suited to bioinformatics, it isn't the only choice nor is it always the best choice. Other programming languages such as C and Java are also used in bioinformatics. The choice of language depends on the problem to be programmed, the skills of the programmers, and the available system.

2.2.2 Rapid Prototyping

Another important benefit of using Perl for biological research is the speed with which a programmer can write a typical Perl program (referred to as rapid prototyping). Many problems can be solved in far fewer lines of Perl code than in C or Java. This has been important to its success in research. In a research environment there are frequent needs for programs that do something new, that are needed only once or occasionally, or that need to be frequently modified. In Perl, you can often toss such a program off in a few minutes or a few hours work, and the research can proceed. This rapid prototyping ability is often a key consideration when choosing Perl for a job. It is common to find programmers familiar with both Perl and C who claim that Perl is five to ten times faster to program in than C. The difference can be critical in the typical understaffed research lab.

2.2.3 Portability, Speed, and Program Maintenance

Portability means how many types of computer systems the language can run on. Perl has no problems there, as it's available for virtually all modern computers found in biology labs. If you write a DNA analyzer in Perl on your Mac, then move it to a Windows computer, you'll find it usually runs as is or with only minor retrofitting.

Speed means the speed with which the program runs. Here Perl is pretty good but not the best. For speed of execution, the usual language of choice is C. A program written in C typically runs two or more times faster than the comparable Perl program. (There are ways of speeding up Perl with compilers and such, but still... .)

In many organizations, programs are first written in Perl, and then only the programs that absolutely need to have maximum speed are rewritten in C. The fact is, maximum speed is only occasionally an important consideration.

Programming is relatively expensive to do: it takes time, and skilled personnel. It's labor-intensive. On the other hand, computers and computer time (often called CPU time after the central processing unit) are relatively inexpensive. Most desktop computers sit idle for a large part of the day, anyway. So it's usually best to let the computer do the work, and save the programmer's time. Unless your program absolutely must run in say, four seconds instead of ten seconds, you're okay with Perl.

Program maintenance is the general activity of keeping everything working: such activities as adding features to a program, extending it to handle more types of input, porting it to run on other computer systems, fixing bugs, and so forth. Programs take a certain amount of time, effort and cost to write, but successful programs end up costing more to maintain than they did to write in the first place. It's important to write in a language, and in a style, that makes maintenance relatively easy, and Perl allows you to do so. (You can write obscure, hard-to-maintain code in Perl, as in other languages, but I'll give you pointers on how to make your code easy for other programmers to read.)

2.2.4 Versions of Perl

Perl, like almost all popular software, has gone through much growth and change over the course of its nearly 15-year life. The authors—Larry Wall and a large group of cohorts—publish new versions periodically. These new versions have been carefully designed to support most programs written under old versions, but occasionally some major new features are added that don't work with older versions of Perl.

This book assumes you have Perl Version 5 or higher installed. If you have Perl installed on your computer, it's likely Perl 5, but it's best to check. On a Unix or Linux system, or from an MS-DOS or MacOS X command window, the perl -v command displays the version number, in my case, Version 5.6.1. The number 5.6.1 is "bigger" than 5; that means it's okay. If you get a smaller number (very likely 4.036), you have to install a recent version of Perl to enable the majority of programs in this book to run as shown.

What about future versions? Perl is always evolving, and Perl Version 6 is on the horizon. Will the code in this book still work in Perl 6? The answer is yes. Although Perl 6 is going to add some new things to the language, it should have no trouble with the Perl 5 code in this book.