Perl编程入门：生物信息学篇

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" Beginning Perl for Bioinformatics 是一本由James Tisdall编写的书籍，专注于介绍如何使用Perl语言在生物信息学领域进行工作。作者James Tisdall具有丰富的背景，包括音乐家、程序员和技术人员的经历，特别是在贝尔实验室进行语音研究时编写程序，并在人基因组项目中使用Perl进行生物信息学分析。他在Mercator Genetics公司通过Perl程序帮助发现了与遗传性疾病血色素沉着症相关的基因，并在费城的福克斯蔡斯癌症中心担任生物信息学经理。最近，他作为Biocomputing Associates和康奈尔大学附属的Burke Research Institute的顾问，致力于研究阿尔茨海默病和帕金森病等神经退行性疾病。" 在这本书中，读者可以期待学习到以下核心知识点： 1. **Perl语言基础**：书中将涵盖Perl编程语言的基础概念，如语法、变量、控制结构、函数和正则表达式，这些都是处理生物信息学数据所必需的。 2. **生物信息学基础知识**：作者可能会介绍生物学的基础知识，特别是与基因组学和分子生物学相关的概念，以便读者能理解如何将Perl应用于生物数据。 3. **数据处理和分析**：由于生物信息学涉及大量数据处理，书中的内容可能包括序列比对、基因预测、进化树构建、统计分析等方法，以及如何用Perl实现这些算法。 4. **Perl在生物信息学中的应用**：书中可能会展示具体的Perl脚本示例，用于解析基因组数据、处理蛋白质序列、执行BLAST搜索、操作GFF或FASTA文件等常见任务。 5. **生物数据库的交互**：Perl常用于与各种生物信息学数据库（如NCBI的Entrez或Ensembl）进行交互，读者将学习如何使用Perl接口来查询和下载数据。 6. **模块和工具**：介绍Perl在生物信息学中常用的模块，如BioPerl，这是一个包含许多生物信息学工具和函数的库。 7. **实践项目**：可能包含实践项目和案例研究，帮助读者将所学知识应用到实际生物信息学问题中，例如基因注释、变异检测或小RNA分析。 8. **问题解决和调试**：教授如何识别和解决在Perl编程中遇到的问题，以及调试技巧，这对于任何编程学习者都是至关重要的。通过这本书，初学者可以逐步建立起将Perl语言应用于生物信息学研究的技能，而有经验的Perl程序员也可以了解如何将他们的技能扩展到这个领域的具体应用。这本书不仅提供技术知识，还展现了Perl在实际科研中的应用价值。

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5. Install the distribution on your computer.

2.3.4 Binary Versus Source Code

When downloading from the http://www.perl.com site, you need to choose between binary or source-code distributions of

Perl. The best choice for installing Perl on your computer is to get an already made binary version of the program, because

it's the easiest to install. However, if no binary is available, or if you want to control the various options of your Perl

installation, you can get the source code for Perl, which is itself written in the C programming language. You then compile

it using a C compiler. But try to find a binary for your particular computer's operating system; compiling from source code

can be complicated for beginners.

2.3.5 Installation

The next sections provide specific installation instructions for specific platforms.

2.3.5.1 Unix and Linux

If Perl isn't installed on your Unix or Linux machine, first try to find a binary to install. At the Downloads page of

http://www.perl.com

, you'll see the subheading Binary Distributions. Select Unix or Linux, and then see if your particular

flavor of operating system has a binary available. Several versions are available, and the web-site instructions should be

enough to get Perl installed once you've downloaded the binary. Most versions of Linux maintain up-to-date Perl binaries

on their web sites. For instance, if you have a Red Hat Linux system, you need to identify which version of the system you

have (by typing uname -a) and then get the appropriate rpm file to download and install. Red Hat has an rpm for Perl that

Red Hat Linux users can install by typing:

rpm -Uvh perl.rpm

(the actual name of the perl.rpm file varies).

If no binary version of Perl is available for your flavor of Unix or Linux, you must compile Perl from its source code. In

this case, starting from the Perl web page, click on the Downloads button and then select Source Code Distribution. The

source code has an INSTALL file with instructions that guide you through the process of downloading the source code,

installing it on your system, compiling the source code into a binary, and finally installing the binary.

As mentioned previously, compiling from source code is a considerably longer process than installing an already made

binary, and requires a bit more reading of instructions, but it usually works quite well. You will need a C compiler on your

computer to install from source code. Nowadays, some Unix systems ship without a complete C compiler. Linux will

always have the free C compiler called gcc installed, and you can also install gcc on any Unix (or Windows, or Mac) system

that lacks a C compiler.

2.3.5.2 Macintosh

The MacPerl installation steps are clearly explained on the MacPerl web page, http://www.macperl.com/

(which you can

also get to from the Perl web page and its Downloads button). Here's a very brief overview.

From the MacPerl page, click on Get MacPerl, and follow the directions to download the application. It will appear on your

desktop. Double-click it to unstuff it. If you don't have Aladdin Stuffit Expander (most Macs already do), this won't work,

and you'll have to go to http://www.aladdinsys.com

to download and install Stuffit.

MacPerl can be installed as a standalone application under the MacOS Finder or as a tool under the Macintosh

Programmer's Workbench; you will probably want the standalone application. Perl Version 5 is available for MacOS 7.0

and later. Details about which Perl version is available for your particular hardware and MacOS version are available at the

MacPerl web page.

2.3.5.3 Windows

Several binaries for different Windows versions are available. Since Windows is closely coupled with Intel 32-bit chips,

these binaries are often called Wintel or Win32 binaries. The current standard Perl distribution is ActivePerl from

ActiveState, at http://www.activestate.com/ActivePerl/

, where you can find complete installation directions. You can also

get to ActivePerl via the Downloads button from the Perl web site. Under the subheading Binary Distributions, go to Perl

for Win32, and then click on the ActivePerl site.

From the ActiveState web site's ActivePerl page, click the Downloads button. You can then download the Windows-Intel

binary. Note that installing it requires a program called Windows Installer, which is available at ActivePerl if it's not already

on your computer.

2.4 How to Run Perl Programs

The details of how to run Perl vary depending on your operating system. The instructions that come with your Perl

installation contain all you need to know. I'll give short summaries here, just enough to get you started.

2.4.1 Unix or Linux

On Unix or Linux, you usually run Perl programs from the command line. If you're in the same directory as the program,

you can run a Perl program in a file called this_program by typing perl this_program. If you're not in the same directory,

you may have to give the pathname of the program, for example:

perl /usr/local/bin/this_program

Usually, you set the first line of this_program to have the correct pathname for Perl on your system, because different

machines may have installed Perl in different directories. On my computer, I use the following as the first line of my Perl

programs:

#!/usr/bin/perl

You can type which perl to find the pathname where Perl is installed on your system.

You can make the program executable using the chmod program: for instance, you can type:

chmod 755 this_program

If you've set the first line correctly and used chmod, you can just type the name of the Perl program to run it. So, if you're in

the same directory as the program, you can type ./this_program. If the program is in a directory that's included in your

$PATH or $path variable, you can type this_program.

[2]

$PATH is the variable used for the sh, bash, and ksh shells; $path is used for csh and tcsh.

If your Perl program doesn't run, the error messages you get from the shell in the command window may be confusing. For

instance, the bash shell on my Linux system gives the error message:

bash: ./my_program: No such file or directory

in two cases: if there really is no program called my_program in the current directory or if the first line of my_program has

incorrectly given the location of Perl. Watch for that, especially when running programs from CPAN (see Appendix A

which may have different pathnames for Perl embedded in their first lines. Also, if you type my_program, you may get this

error message:

bash: my_program: command not found

which means that the operating system can't find the program. But it's there in your current directory! The problem is

probably that your $PATH or $path variable doesn't include the current directory, and so the system isn't even looking in

the current directory for the program. In this case, change the $PATH or $path variable (depending on which shell you're

using), or just type /my_program instead of my_program.

2.4.2 Macs

On Macs, the recommended way to save Perl programs is as "droplets"; the MacPerl documentation gives the simple

instructions. Basically, you open the Perl program with the MacPerl application and then choose Save As and select the

Type option Droplet.

You can drag and drop a file onto a droplet in order to use the file as input (via the @ARGV array—see the discussion in

Chapter 6

The new MacOS X is a Unix system on which you have the option of running Perl programs from the command line as

described earlier for Unix and Linux systems.

2.4.3 Windows

On Windows systems, it's usual to associate the filename extension .pl with Perl programs. This is done as part of the Perl

installation process, which modifies the registry settings to include this file association. You can then launch

this_program.pl by typing this_program in an MS-DOS command window or by typing perl this_program.pl. Windows has

a PATH variable specifying folders in which the system looks for programs, and this is modified by the Perl installation

process to include the path to the folder for the Perl application, usually c:\perl. If you're trying to run a Perl program that

isn't installed in a folder known to the PATH variable, you can type the complete pathname to the program, for instance perl

c:\windows\desktop\my_program.pl.

2.5 Text Editors

Now that you've set up your computer and installed Perl, you need to select and learn the basics of a text editor. A text

editor is used to type documents, such as programs, and to save the contents of those documents into files. So to write a Perl

program, you need to use a text editor. This can be a medium-sized learning job if you have never used an editor before,

although some text editors are easy to learn. Here are some examples of the most popular editors, arranged by operating-

system type:

Unix or Linux

vi and emacs are complex (but very good) editors. pico, xedit, and several others (nedit, gedit, kedit)

are easy to use and simple to learn but less powerful. There is also a free, Microsoft Word-

compatible editor included in StarOffice (but be sure to save your files as ASCII or text-only).

Macintosh

The built-in editor that comes with MacPerl is fine. There is also a nice commercial editor called

BBEdit that is optimized for Perl, as well as a freeware version called BBEdit Lite. You can also

use the Alpha shareware editor or Microsoft Word (be sure to save as ASCII text only).

Windows

Notepad works satisfactorily and may already be familiar; Microsoft Word is also usable, but

always save as ASCII or text-only. Emacs on Windows is highly recommended for Perl

programming on Windows-based computers, but it's a little complicated to learn. There are many

other editors as well; I use a free version of the Unix editor vi called vim that has been ported to

Windows.

Many other text editors are available. Most computers come with a choice of several editors. (Many programmers try their

hand at writing an editor or extending an already existing editor at some point in their careers, so the choices are truly

legion.)

Some editors are very simple to learn and use. Others have a huge variety of features, their own instruction books and

discussion groups and web sites and so on, and can take quite a while to learn. If you're a new programmer, pick an easy

one and save yourself the headache. Later, if you feel adventurous, you can graduate to a fancier editor with features that

can speed your work. Not sure what is available on your computer? Ask for help from a programmer or another user, or

consult the documentation that came with your computer system.

2.6 Finding Help

Make sure you have the necessary documentation. If you installed Perl as outlined earlier, documentation is installed as part

of the general Perl installation, and the instructions that come with your Perl distribution explain how to get the

documentation. There is also excellent online documentation; look for it at the Perl home pageError! Hyperlink reference

not valid..

Programming resources are places to look for answers to programming questions. Perl resources are essential to doing Perl

programming. Check out Appendix A

to learn where to find resources such as books, online documentation, working

programs, newsgroups, archives, journals, and conferences.

As you get involved in programming, you will learn the most important books, web sites, Internet newsgroups and their

searchable archives, local gurus (experts in the subject at hand), and program documentation. This includes programming

manuals (printed or online) and frequently asked question (FAQs).

Most languages have a standard document set that includes the whole story about the language definition and use. Perl's is

included with the program as the online manual. Although programming manuals often suffer from poor writing, it's best to

be prepared to dig into them. A well-honed ability to skim is a great asset. The Perl manual isn't bad; its main problem is

that, as with most manuals, all the details are there, so it can be a bit overwhelming at first. However, the Perl

documentation does a decent job of helping the beginner navigate, by means of tutorial documents.

Finally, I urge you, the beginning programmer, to find some experienced Perl programmer who can answer the occasional

question. This may be your teacher or teaching assistant in a course, a coworker, someone down at the local computer store,

or someone replying to your posting on an online newsgroup (there are newsgroups specifically for Perl beginners).

Chances are that an occasional conversation with an experienced user can save you many hours of chasing deadends during

your initial learning stages. Many programmers are happy to lend a hand or offer advice to beginners, there's a friendly and

collegial atmosphere that prevails in the programming community.

Be warned, however: experts can become irritated at people who continually pose questions whose answers are readily

available in FAQs and other standard documentation. You might sometimes see the advice to RTFM—acronym for Read

The F(ine) Manual—in response to such questions. So do a little checking around in the FAQs before repeatedly asking for

someone's valuable time.

(I can't resist the occasional anecdote.) At my first programming job, which I took to learn programming, I was stumped by

a problem for which there seemed to be no obvious solution. I approached the person who had been cited as the best

programmer in the laboratory. I carefully explained my predicament as he patiently listened. When I was done, he smiled

and advised, "Be a man. Do it yourself." I was crestfallen and retired in confusion. But as it turned out, his advice was given

with tongue in cheek, and he later approached me and gave me pointers that led to a solution.

Chapter 3. The Art of Programming

This chapter provides an overview of how programmers accomplish their jobs. If you already have Perl installed, and you

want to get started writing programs for bioinformatics, feel free to skip ahead to Chapter 4

Just as visitors to a biology lab tend to have a clueless awe of "all those test tubes," so the newcomer to programming may

regard the world of the programmer as a kind of arcane black box full of weird terminology and abstruse skills. So, to make

the whole enterprise a little more congenial, let's take a short tour of some important realities that affect all programmers.

Two of the most important are practical strategies that good programmers use and where to go to find answers to questions

that arise while you are programming. Using a couple of brief narrative case studies, we'll look at how programmers find

solutions to problems. Appendix A

lists some of the best Perl and bioinformatics resources to help you solve your particular

problems.

3.1 Individual Approaches to Programming

What's the best way to learn programming? The answer depends on what you hope to accomplish. There are several ways to

get started. You can:

• Take classes of many different kinds

• Read a tutorial book like this one

• Get the programming manuals and plunge in

• Be tutored by a programmer

• Identify a program you need

• Try any and all of the above until you've managed to write the program

The answer also depends on how you choose to learn. Some people prefer classes, because the information is often

presented in a well-organized way, and questions can be answered by the teacher. Others learn best with self-paced study.

Some things about learning to program are common to all these approaches. If you've never programmed at all, the

information in the following sections is a "heads-up" about what's ahead.

3.2 Edit—Run—Revise (and Save)

The most important thing about programming is that it's a hands-on learning activity such as dancing, playing music,

cooking, or some other family-oriented activity. You can read about it, but you can't actually do it until you actually do it.

While learning to program in Perl, you need to read about how Perl works, as you will in the chapters that follow. You also

need to look at plenty of examples of programs. But you especially need to attempt to write your own programs, as you are

asked to do in the exercises at the end of the later chapters. Only this kind of direct experience will make you a programmer.

So I want to give you an overview of the most important tasks involved in writing programs, to help you approach your first

programs with a clearer idea of what's really involved.

What exactly will you be doing at the computer? The bulk of a programmer's work involves the steps of writing or revising

a program in an editor, then running the program and watching how it behaves, and on the basis of that behavior going back

and revising the program again. A typical programmer spends more than half of his or her time editing the program.

3.2.1 Saves and Backups

Once you have even a few lines of code written, it's important to save it. In fact, you should always remember to save a

version of your program at regular intervals during editing, so if you make a bunch of edits and the computer crashes, you

don't lose hours of work. Also, make sure you back up your work on another disk. Hard disks fail, and when yours does, the

information on it will be lost. Therefore it's essential to make regular (daily) backups of your work onto some other

medium—tape, floppy disk, Zip disk, another hard disk, writable CD—whatever, just so you won't lose all your work if a

disk failure occurs.

In addition to backups of your disks, it's also a good idea to save a dated version of your program at regular intervals. This

will allow you to go back to an earlier version of your program should that prove necessary.

It's also a good idea to make sure the backups you're making actually work. So, for instance, if you're backing up to a tape

drive, try restoring the files from your tape drive every once in a while, just to make sure that the software and the tapes

themselves are all working. You may also want to print out ("make a hardcopy") of your programs at regular intervals for

extra insurance against system failures. Finally, it's good policy to keep the backups somewhere away from the computer,

so in case of fire or other disaster, the backups will be safe.

3.2.2 Error Messages

Fixing errors is an essential step in writing programs. After you've written and edited a program, the next step is to run it to

see if it works. Very often, you'll find that you've made some typographical error, like forgetting to put in a semicolon. As a

result, your program isn't valid, and you'll get various error messages from the system. You then have to read the error

messages and reedit your program to repair the offending code.

These error messages are sometimes rather cryptic. In the event of an error, the Perl interpreter may have some trouble

knowing exactly where you went wrong. It may only recognize that there is something wrong. So it guesses where the

problem is, and in the process, it may give you some extraneous information.

The most important thing about using error messages is to look at the first one or two error messages and ignore the rest; fix

the top problems, and try running the program again. Error messages are often verbose and can run on for several pages.

Just ignore everything but the first errors reported. Another important point is that the line numbers reported in those first

error messages are usually right. Sometimes they're off by a line, and they're rarely way off. Later on, we'll practice

generating and reading error messages.

3.2.3 Debugging

Perhaps your edits created a valid program, and the Perl interpreter reads in your program and runs it. You find, however,

that the program isn't doing what you want it to do. Now you have to go back, look at the program, and try to figure out

what's wrong.

Perhaps you made a simple mistake, such as adding instead of subtracting. You may have misread the documentation, and

you're using the language the wrong way (reread the documentation). You may simply have an inadequate plan for

accomplishing your goal (rethink your strategy and reprogram that part of the code). Sometimes you can't see what's wrong,

and you have to look elsewhere (try searching newsgroup archives or FAQs or asking colleagues for help).

For errors that are difficult to find, there are programs called debuggers that allow you to run the program step by step,

looking at everything that's happening in the program. (Chapter 6

takes an in-depth look at Perl's debugger.)

There are other tools and techniques you can use. For instance, you can examine your program by adding print statements

that print out intermediate values or results. There are also special helper programs that can observe your program while it's

running and then report about it, telling you, for instance, about where the program is spending most of its time. These tools,

and others like them, are essential to programming, and you need to learn how to use them.

3.3 An Environment of Programs

Programming is an exercise in problem solving. It's an iterative, gradual process. Although it can be done by one person

alone, it's often a social activity (this surprises many newcomers). It requires developing specific problem-solving skills and

learning a few tools. Programming is sometimes tricky and can be frustrating. On the other hand, for those with an aptitude,

there's a great sense of satisfaction that comes from building a working program.

Computer programs can be many things, from barely useful, to aesthetically and intellectually stimulating, to important

generators of new knowledge. They can be beautiful. (They can also be destructive, stupid, silly, or vicious; they are human

creations, after all.) Because writing a program is an iterative, building, gradual process, there can be real satisfaction in

seeing the work unfold from simple beginnings to complete structures. For the beginning student, this gradual unfolding of

a new program mirrors the gradual mastery of the language.

As our culture began writing and accumulating programs in the middle of the 20th century, a programming environment

began to develop. Gradually, we've been accumulating a substantial body of procedural knowledge. Programs often reflect

the fact that they swim in waters populated by many other programs, and beginning programmers can expect to learn a lot

from this environment.

3.3.1 Open Source Programs

As programming has become important in the world, it has also become economically valuable. As a result, the source code

for many programs is kept hidden to protect commercial assets and stymie the competition.

However, the source code for many of the best and most used programs are freely available for anyone to examine. Freely

available source code is called open source. (There are various kinds of copyrights that may attach to open source program

code, but they all allow anyone to examine the source code.) The open source movement treats program source code in a

similar manner to the way scientists publish their results: publicly and open to unfettered examination and discussion.

The source code for these programs can be a wonderful place for the beginning programmer to learn how professional

programmers write. The programs available in open source include the Perl interpreter and a large amount of Perl code, the

Linux operating system, the Apache web server, the Netscape web browser, the sendmail mail transfer agent, and much

more.

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