Perl & Genomics

This is the landing page for the fourth laboratory, here at the Paolotti. We missed you!

Remember to keep this page updated regularly, as we are going to put some updates in here.

Let’s start, as usual, with the “appello Nome Cognome” command from the shell, that makes you checking in in the system, and don’t forget the “goodbye” command at the end. Then create a lab04 directory in your home folder. You’ll save scripts there. Ready?

Homework review

A major task for today is homework review.
Some of you has been brilliant, not only in correctly solving the exercises (this is the least important part) but also doing them regularly and not at the end, and asking questions via e-mail or comments. Good guys! We are proud of you.
We are going do the review both interactively (meaning us talking with you) and as a self service kiosk.

1. The latter method implies that you are going to read the solutions of some of the exercises. So, start reviewing your homeworks using the solutions, and wait for instructors to ask live questions. Simple, uh?
2. We are not going to solve hw5, because solving the others you should be able to complete it at home before next lab.
3. We also have a small post on Perl hashes, in case you want to better understand it.

We bet that this part could require the whole afternoon for some, and a few minutes for the tech-savvy nerds. So,… we want to be flexible and we ask you to take your time and not to rush.

To view your homework type “compitino hw3” or whatever from the shell.

What’s next

We are going to introduce a couple of important concepts for Perl programmers. A couple of things to make our Perl programs powerful and useful.

1) How to pass arguments to a script – that is how to give some parameters to our program so that they perform custom calculations for us.

2) How to read a file from a script – cool! we are going to be able to read, and thus elaborate, text files (like a FASTQ or SAM file). This is an optional part for the fastest fellows. We are going to do this tomorrow in class.

 A final comment to the homeworks

Some of you – as we said earlier – has been regular submitting homeworks. We think this is a very good way to approach a new discipline as programming. This is the current situation:

To our opinion having done the first homeworks (that is 1 to 4) is quite fine.