Question: How To Initiate Learning Perl?
8
gravatar for gaurav.amit30
7.3 years ago by
gaurav.amit3080 wrote:

I am new to Bioinformatics field. I am doing some kind of Genomics work. So I am trying to learn Perl and Unix. Can anyone suggest me from where to initiate these? Some basic books or tutorial online or some other web pages? Thanks.

perl • 3.3k views
ADD COMMENTlink modified 4.9 years ago by andrew20 • written 7.3 years ago by gaurav.amit3080
7

I love perl, I learned bioinformatics using perl, and in crunch time it's what I fall back to. But my suggestion for people entering bioinformatics now: Also consider other programming languages. On the Unix side, learn to use awk and sed for any line-by-line text processing and you'll be amazingly efficient. Good luck...

NOTE: I removed my unintended flamebait. Please, we all have better things to do that engage in language wars. My intent (poorly stated) was to add a side note that Perl isn't the only option in bioinformatics. It was a perspective I hadn't seen expressed in the other comments and answers here, so I thought it might be useful to the OP. I apologize for starting this digression, and I'm hoping it ends here.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Andrew Su4.8k
2

Admirable, Andrew -- since there are many many places on the web already to find the latest installment of this old flamewar. This is a Yankees-RedSox, Coke-Pepsi, Slackware-Ubuntu etc type of discussion, and I think we all agree it's counterproductive. There are so many ways to get any job done -- and I agree anyone starting out in bioinformatics should develop skills in several languages. So, thumbs up.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Alex Paciorkowski3.3k
1

I prefer python over perl also and I think it is probably an easier starter language. But I do agree with Michael. After learning a few languages and coming to grips with the fundamental logic, it all comes down to personal preference. Syntax is pretty easy to pick up after a while.

ADD REPLYlink written 7.3 years ago by Damian Kao15k
2

Programming in python is also a better way to learn programming in general. The code is more explicit: I mean someone who understands pseudo-code can understand python. In addition, oriented object programming is a possibility you have in python and not in perl. However I would not recommend the use of biopython for dealing with big files which is nowadays a serious drawback. That was to support Andrew's advice ;-)

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Manu Prestat3.9k
2

OO Perl has been around for a while...

http://perlmonks.org/?node=Tutorials#Object-Oriented-Programming

http://www.amazon.com/Object-Oriented-Perl-Comprehensive-Programming/dp/1884777791/ref=sr_1_1?ie=UTF8&qid=1343358250&sr=8-1&keywords=Object+Oriented+Perl

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Alex Paciorkowski3.3k
2

Moose is the best way to do OOP in modern Perl.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Tom Walsh550
3

Best thing I can tell you is to actually WRITE the code instead of only reading over other people's/book's code. For a beginner, reading and understanding other people's code is completely different from actually writing the code yourself. I've noticed a lot of people would attend programming lectures and understand the material, but when it comes to writing code, they can't do it. Fundamental code logic is essential, but also learn the syntax by writing code independently.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Damian Kao15k
1

I like this for unix-introduction: http://www.softlab.ntua.gr/facilities/documentation/unix/docs/sh.ps

ADD REPLYlink written 7.3 years ago by Biomonika (Noolean)3.1k
7
gravatar for Michael Dondrup
7.3 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

Congratulations, you have chosen the right language!

 

see:

  perldoc perl
  perldoc perlintro

for an overview.

Books:

  • The O'Reilly Camel and esp. Lama books are quite good. Beginning Perl for Bioinformatics not recommended, doesn't cover BioPerl, and dated.

Also, after learning perl you will need to develop some BioPerl skills.

ADD COMMENTlink modified 4.2 years ago • written 7.3 years ago by Michael Dondrup46k

Thanks Michael sir!! I would be in touch of *Biostar for my further problems while rading and understanding it.

ADD REPLYlink written 7.3 years ago by gaurav.amit3080
6
gravatar for Tom Walsh
7.3 years ago by
Tom Walsh550
United Kingdom
Tom Walsh550 wrote:

Have a look at the Unix & Perl Primer for Biologists.

The Lama book is good for Perl beginners - be sure to get the most recent (6th) edition.

Perl has changed a lot in recent years so I would avoid books that are more than a few years old. Modern Perl is a good introduction to current best practices and you can download a copy for free.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Tom Walsh550
2
gravatar for swbarnes2
7.3 years ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

1) Identify problem you want to solve. Pick something simple, like manipulating a large text file.

2) Read books, solve it

3) Read some more, and solve it a new way.

Personally, I didn't find the O'Reilly bioinformatics books all that helpful. I started with Learning Perl.

ADD COMMENTlink written 7.3 years ago by swbarnes27.0k
1
gravatar for Bert Overduin
7.3 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

This is a great introduction to Perl:

http://sofiarobb.com/learning-perl-toc/

ADD COMMENTlink written 7.3 years ago by Bert Overduin3.6k
1
gravatar for Gjain
7.3 years ago by
Gjain5.4k
Munich, Germany
Gjain5.4k wrote:

Hi Gaurav,

Perl is a good place to start. I would recommend these two resources that are available:

  1. Beginning Perl (Free Online Book)

    Perl is a well-established programming language that has been developed through the time and effort of countless free software programmers into an immensely powerful tool that can be used on pratically every operating system in the world. Perl started out as the "Swiss army knife" of computer languages and was used primarily by system administrators, but over time it's grown into an immensely robust language used by web-developers and programmers worldwide. It's also a great way to learn programming techniques and develop your own style of coding.

  2. Beginning Perl for Bioinformatics

    Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab.

    enter image description here

I hope this helps.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Gjain5.4k

I cannot not recommend Beginning Perl for Bioinformatics, it does not cover BioPerl last time I checked. I think that way, it's better to use a universal perl book.

ADD REPLYlink written 7.3 years ago by Michael Dondrup46k
1

I must agree, "beginning perl for bioinformatics" is quite outdated.

ADD REPLYlink written 7.3 years ago by Timtico330
1

Thanks Michael and Timtico for the update. I used it couple of years ago when i started learning Perl. It was useful then.

ADD REPLYlink written 7.3 years ago by Gjain5.4k

I think you will be able to learn perl with it still, but if you needed to spend money on a book, I believe you will fare better with the a general introduction via the Lama book. +1 for your first link though, because it's a free online book.

ADD REPLYlink written 7.3 years ago by Michael Dondrup46k
1

Thanks Michael. I used the first link for a presentation for biologists without programming background to give an introduction to Perl. They seemed to like that free and comprehensive online book.

ADD REPLYlink written 7.3 years ago by Gjain5.4k
1
gravatar for Arun
7.3 years ago by
Arun2.3k
Germany
Arun2.3k wrote:

Most of the biologists / non-programmers have difficulty in diving into this jargon and understanding concepts. I know quite a few of them who preferred working with examples. And they particularly found the book Perl by Example by Ellie Quigley very useful . It has staggering amount of examples and every concept is introduced as such. This should be a starting book if you are new to programming as well, I believe. It has some typos (or had in the earlier version), nevertheless, it should be an excellent starter.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Arun2.3k
1
gravatar for andrew
4.9 years ago by
andrew20
United Kingdom
andrew20 wrote:

Sorry, but it took me a while to put together a response to your question:

https://geekuni.com/

:)

ADD COMMENTlink written 4.9 years ago by andrew20
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