it very good indeed, I understand 90%.

very good

Thanks again!!.

Great!!!! I like those tutorials !

thanks, i've gone through your first 2 tutorials and honestly this has been more helpful than anything else i've found so far. they're much appreciated

Hi, thank you so much for your series! I'm experiencing some problems when trying to use the DNA methods though. In your commented lines, you suggest using these methods as in dna.transcribe. But that does not return any output on the screen. So, in this case, do we need to insert a puts method somewhere inside the method definition? Thank you so much and sorry such a basic question (I'm a ruby newbie).

Thank you

Hi Ref,

Glad you enjoyed the videos.

In regards to question 1: // works equally well instead of /\B/ (there must have been a typo somewhere). But basically /\B/ means "non-word boundary". But (//) seems to be better suited for extracting each character, so I would just use that (for example you see)

"words\t\nbleh blah".split(//)

=> ["w", "o", "r", "d", "s", "\t", "\n", "b", "l", "e", "h", " ", " ", " ", "b", "l", "a", "h"]

while

"words\t\nbleh blah".split(/\B/)

=> ["w", "o", "r", "d", "s\t", "\nb", "l", "e", "h ", " ", " b", "l", "a", "h"]

2.) You're absolutely right. @seq will not be modified even if I use collect!, so I might as well have used collect instead.

Regards,

Chinmoy.

Hello chingav,

Thanks for this great series. These videos really helped clarify some stuff for me but I have two itches that need further clarification :)

1-) What does string.split(/B/) do or rather how is it different from string.split(//) ?

( Actually I was playing around with this code and split(/B/) wasn't working for me.

I checked ruby-doc.org and the example there uses split(//) to split "hello" into "h","e","l","l","o" so I changed /B/ to // and it started working.

Now, since I am a total ruby newb who is clueless about regex I am left wondering what was the /B/ supposed to do :) )

2-) Why are you using collect! ? I mean collect! is supposed to change the original object you are operating on right? Well that's not what you really need in this case I guess. I mean the original DNA sequence should not change everytime we ask for its complement. AND collect! can't really change the @seq because we split it into 5 different strings and convert those strings to an array. I don't know the innards of ruby but I guess the string object we start with is not the same object as the array object we end up with so using collect! or collect should have no difference. Am I right?

Actually now that I think about it... Isn't collect about applying a function to each member of a set and producing a different set which maps 1 to 1 to the source set? If it's about producing a new set, is there a reason to have collect! ?

Thanks again for the great series!

Cheers,

Ref

Hi Chinmoy - great, debugging videos will be an excellent addition! That's a skill that is always hard to learn by reading and so much easier to learn by seeing!

Ian.

Hello everyone,

Coming Soon-->Screencast 6 and 7: I made them, but I will have to edit them, upload them, etc.

These cover using the built-in ruby debugger, using ruby-debug from the Data Noise blog, using the Tracer library to trace the execution of code and help pinpoint trouble spots, Unit Testing your code, and a really quick overview on showing the differences between Tkinter and Ruby/Tk when it comes to drawing lines on a canvas(I'll get into the details of this in a later screencast.

I haven't forgotten about the CSV library either. I will cover it later(there were a lot of votes for debugging, so I went ahead and covered those.

Some of you might have had trouble accessing the Box widget on my blog. It should be fixed now. Let me know if you have trouble.

Hello again,

I just remembered that I ported another Python script(this one was harder to do, so it might be more interesting). If anyone wants to look at it before I incorporate it into a future screencast, it is available at http://gavmacprogramming.wordpress.com/2007/04/19/porting-peter-norvigs-martin-shuffle-algorithm/

It is a Markov Decision Process experiment ported from the Python code in Dr.Peter Norvig's article (he is a famous Google researcher)

Regards,

Chinmoy.

Hi Ian and everybody,

Sure. I'll try to work in more ported code as examples.

Regards,

Chinmoy.

Hi again Chinmoy. Great to see you show a bit of ported Python bioinformatics code!

Showing how to get started converting code to another language is nice, I hope we can get more of this sort of content (e.g. from Java to xxx...).

Cheers,

Ian.