Home Bioinformatics • Download e-book for iPad: Beginning Perl for Bioinformatics by James Tisdall

Download e-book for iPad: Beginning Perl for Bioinformatics by James Tisdall

By James Tisdall

ISBN-10: 0596000804

ISBN-13: 9780596000806

With its hugely constructed capability to realize styles in information, Perl has turn into probably the most renowned languages for organic info research. but when you're a biologist with very little programming adventure, beginning out in Perl could be a problem. Beginning Perl for Bioinformatics is designed to get you fast over the Perl language barrier through drawing close programming as an enormous new laboratory ability, revealing Perl courses and strategies which are instantly valuable within the lab. every one bankruptcy makes a speciality of fixing a specific bioinformatics challenge or type of difficulties, beginning with the best and lengthening in complexity because the ebook progresses. each one bankruptcy comprises programming routines. through the tip of the ebook you'll have a fantastic knowing of Perl fundamentals, a set of courses for such projects as parsing BLAST and GenBank, and the abilities to tackle extra complicated bioinformatics programming.

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They typically include a discussion of the overall purpose and design of the program, examples of how to use the program, and detailed notes interspersed throughout the code explaining why that code is there and what it does. In general, a good programmer writes good comments as an integral part of the program. You'll see comments in all the programming examples in this book. This is important: your code has to be readable by humans as well as computers. Comments can also be useful when debugging misbehaving programs.

However, one big warning about modifying existing code: depending on how much alteration is required, it can sometimes be more difficult to modify existing code than to write a whole program from scratch. Why? Well, depending on who wrote the program, IT-SC 32 it may be difficult just to see what the different parts of the code do. You can't make modifications if you can't understand what methods the program uses in the first place. ) This factor alone accounts for a large part of the expense of programming; many programs can't be easily read, or understood, so they can't be maintained.

The name gives you full access to the data. Example 4-1 shows the entire program. Example 4-1. /usr/bin/perl -w # Storing DNA in a variable, and printing it out # First we store the DNA in a variable called $DNA $DNA = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; # Next, we print the DNA onto the screen print $DNA; # Finally, we'll specifically tell the program to exit. IT-SC 43 exit; Using what you've already learned about text editors and running Perl programs in Chapter 2, enter the code (or copy it from the book's web site) and save it to a file.

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Beginning Perl for Bioinformatics by James Tisdall

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