15 replies to this topic

[K.B.]

Hello,
Having a little bit more free time on my hands, at least for now, I'm thinking about starting to learn some programming language. My idea is to use it for writing small dedicated programs to help with my lab work and perhaps some DIY/home improvement/"gadget hacking"/"mad scientists" stuff. Which one would you advise me to learn?

[HomeBrew]

Perl.

[Adrian K]

Hi HomeBrew,
I heard there is also Bio-Perl... which is better? I'm a total noob in programming....but i wish to learn.

[HomeBrew]

BioPerl is a collection of Perl modules written to facilitate bioinformatics programming in Perl.  The modules themselves are written in Perl.  A Perl module is just a pre-written piece of code that one can call from within their main program to perform a function, thus saving the Perl programmer from having to re-invent the wheel.

For example, if in my Perl program I wanted to get information from a BLAST results file, I could write my own Perl code to parse this file and return all the various pieces of data for me, or I could just use the appropriate BioPerl module, e.g.:

#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;  # This line loads the BioPerl module SearchIO

my $in = new Bio::SearchIO(-format => 'blast', -file => "your_favorite_file.blast");

while (my $result = $in->next_result) {
	while (my $hit = $result->next_hit) {
		while (my $hsp = $hit->next_hsp) {
			print "Hit name: " . $hit->name . "\n";
			print "HSP start (hit): " . $hsp->start('hit') . "\n";
			print "HSP end (hit): " . $hsp->end('hit') . "\n";
			print "HSP start (query): " . $hsp->start('query') . "\n";
			print "HSP end (query): " . $hsp->end('query') . "\n";
			print "HSP length: " . $hsp->hsp_length . "\n";
			print "number of identical residues: " . $hsp->num_identical . "\n";
			print "number of conserved residues: " . $hsp->num_conserved . "\n";
			print "strand: " . hit->strand . "\n";
			print "sequence of hit: " . $hsp->hit_string . "\n";
		}
	}
}

[Thensome]

I worked as a developer before going into bio. Although I love perl, I cannot recommend it. Go with python. Much clearer syntax, and so many systems comes with python api these days.

[HomeBrew]

That may be (clearer syntax, etc.) but take a look at the bioinformatic journals -- if code is released, it's usually in Perl...  So, while Python may be a technically superior language in your opinion, Perl is much more widely used in bioinformatics, thus learning it is more beneficial.

But, in any event, it's got to be Perl, Python, or Ruby, if you're looking for a scripting language...

[Adrian K]

HomeBrew, on Jul 13 2010, 01:35 AM, said:

That may be (clearer syntax, etc.) but take a look at the bioinformatic journals -- if code is released, it's usually in Perl...  So, while Python may be a technically superior language in your opinion, Perl is much more widely used in bioinformatics, thus learning it is more beneficial.

But, in any event, it's got to be Perl, Python, or Ruby, if you're looking for a scripting language...

o_O  
==''

Perl, Ruby, Phyton, Bioperl... is endless... I wish I learn at least one of this...

Any idea or good books (Perl for dummies???) I can begin with?
LOL

[HomeBrew]

adrian kohsf, on Jul 12 2010, 07:51 PM, said:

Any idea or good books (Perl for dummies???) I can begin with?

Well, the classic starting book for Perl is Programming Perl, aka "the Camel book", now in its 3rd edition.  This is a comprehensive book, covering all aspects of Perl.  One of the authors, Larry Wall, is the creator of Perl.

For a quick-start on bioinformatics in particular, Beginning Perl for Bioinformatics is pretty good too, but a bit dated.

[Adrian K]

Thanks ya.

[pcrman]

I agree with HomeBrew that perl is the right one to start with. Of course if you want to create some web based applications, php is another laugauge you must learn. The good news is that once you know perl or any programming language, learn other languages is a piece of cake.

[DELETEMYACCOUNTPLEASE]

use python ! perl

Then, if you want to do web stuff, play with Django - nicer than perl catalyst IMO.

perl is great but lack of easy use of objects is annoying (including moose)

I used perl - currently use python + django - scala/java and a little bit of clojure.

I would also suggets that you use Learning Perl - avoid the "* for bioinformatics" books because they don't teach you how to program.

[chromatin]

I have been programing in Perl for about a year. My first programming language. I like it. However, I my computer friends recommend Python. It has cleaner syntax, should be easier to learn. However, it is not a big deal. Once you know one language, learning a second one is much easier if necessary. Perl is more common in bioinformatics and has a lot of available modules (programs that other wrote and publicly available). Enjoy it. It's very much fun.
http://www.bioprotocols.info

[semin]

If you are to learn Python, have a look at Bioinformatics Programming Using Python by Mitchell L. Model (from Oreilly).

[davidiphone5]

I've used LISP to develop IA algorithms several years ago. Is it still in use?

[DELETEMYACCOUNTPLEASE]

Clojure is a lisp, it seems to be gaining popularity while dropping some (of(the parens)).