Have a look at this excellent introduction to Unix and Perl from Ian Korf's lab: http://korflab.ucdavis.edu/Unix_and_Perl/
For BioPerl specifically, you'll want to take a look at the HOWTOs on the BioPerl wiki to see some worked examples.
The Beginning Perl for Bioinformatics by Tisdall is probably a must-have for biologists wanting to learn Perl, even though it is a bit out-dated now.
EDIT: ⬆ This Tisdall book suggestion is really bad advice, so I crossed it out. It was great when it was first released into a world with no BioPerl, but everything in this book teaches the old, bad ways of doing things. It is so common that is worth mentioning that and leaving a note in place. Instead, take a look at the Modern Perl book, Beginning Perl by Curtis Poe, or Learning Perl by brian d foy.
Note that the Unix and Perl reference mentioned above is now a published book. There is a book website with more details on obtaining the print version.
Teach Yourself Perl in 21 Days and Beginning Perl are now more than 10 years old and Perl has changed a great deal since they were published.
I would recommend these books as good introductions to Perl as it is now:
There is also a new edition of Programming Perl (the O'Reilly Camel book) just out.
Martin Krzywinski offers a really good 'Bioinformatics Perl Workshop' and he posts all his materials online. He covers too many topics to list here but his intro to perl includes scalar variables, text manipulation and regular expressions, lists, arrays, context, hashes, sorting, file I/O, subroutines, special variables, and string manipulation. Other courses include more intermediate perl topics, effective use of map, sort and grep in Perl, introductions to Unix, data mining and analysis at the command line, prompt tools, introductions to CGI and mod_perl, and more.
His website is a little confusing to navigate at first but once you figure it out, its a very rich resource for tutorials, tips and sample code.
There are many resources you can look at:
- Teach Yourself Perl 5 in 21 days by David Till
Beginning Perl by Simon Cozens(FREE). The book will cover:
Installing Perl on Windows and UNIX
- Making use of online Perl resources like CPAN
- First principles in programming and the Perl syntax
- Working with files and databases
- Writing web pages in Perl
Using Perl as an object-oriented language
You should also look at previous Biostar posts like:
- How to use Bioperl
I hope this helps.
Self promotion here, but I'd certainly like bioinformatics experts to let me know how they find my Perl courses (especially Perl Essentials) https://geekuni.com/ Let me know if it needs more in the way of regular expressions - any good examples to work off would be a bonus!