Who can program (specifically, in Perl)?

[Malaclypse]

i have never worked with perl, so anything i'll say now could be total bullshit.

anyway,

1. it's usual that DNA sequences won't come out in neat multiples of three, and there's actually no reason to test for that in the beginning. you'd have to truncate any trailing 1 or two bits, however.
2. you can probably reuse the nucleotide checking block for the second sequence without having to copy and paste the code. don't ask me how though, i don't know shit about perl.
3. same goes for basically all larger building blocks of the program - instead of just copying the source for 1st and 2nd sequence, you'd rather out-source them into procedures (if there's any such thing in perl) and reuse them, only changing the input string (the sequence)

a thought on usability:
give the option to read from a file, so you won't bother people to type all these letters. also, you could get rid of the double input to make sure everything was typed down correctly.

 

[Zack]

@Son of God- I would've really liked to see the star mass program, sonofgod. Astronomy is what I plan to study in the future, and I love it.

@Undo: Your program looks mighty cool, too bad I can't understand it!

 

[Nemesis_lxix]

I work with C++ a lot.

 

[Zack]

I'm gonna go to a Genomics lecture this weekend, I'll let you know how it goes.

 

[BastardSonOfGod]

Hahaha Ok Zack... I will ask to my brother about it... maybe he can find it!

 

[Zack]

Yes, thank you, that would be great!

 

[Magrathean]

I'm gonna go to a Genomics lecture this weekend, I'll let you know how it goes.

So how did it go?

 

[Magrathean]

1. it's usual that DNA sequences won't come out in neat multiples of three, and there's actually no reason to test for that in the beginning. you'd have to truncate any trailing 1 or two bits, however.

I know. It would take some more code to make a program that can do that (a thought: i could even let the user decide whether the first base he enters is actually the first, second or third base in its codon). Thanks for the idea. I'll be sure to mention you when i release the final version.

2. you can probably reuse the nucleotide checking block for the second sequence without having to copy and paste the code. don't ask me how though, i don't know shit about perl.

Afaik, i can't do that since the array i use for the first sequence ($seq1[$nt]) and the one i use for the second sequence are two separate ones. I'm not a Perl expert, though, so maybe there's a way i don't know about. A thought would involve using a single array twice the size of the ones i'm using and a marker to tell the program where the first sequence ends and the second one starts. Again, thanks for the idea.

3. same goes for basically all larger building blocks of the program - instead of just copying the source for 1st and 2nd sequence, you'd rather out-source them into procedures (if there's any such thing in perl) and reuse them, only changing the input string (the sequence)

There are procedures in Perl. In the original version of my program (not on this thread), i'd used procedures rather than repeated code. When my program didn't work, i thought it might be due to a syntax error or something in the procedures part (i later found out that the procedures part was ok and that the problem involved a typo where one of the variables went). I think i still have the old code, so i might be able to copy the procedures code to the new one.

a thought on usability:
give the option to read from a file, so you won't bother people to type all these letters. also, you could get rid of the double input to make sure everything was typed down correctly.

I'd thought about the read-from-file option. I still don't know how to do that, so it'll take a bit more time and tutorial-reading than the other ideas you've given me (the ones above) and the ones i've had (ability to insert gaps (using the '-' symbol; i.e. some sequences are larger than others) and calculation of similarity percentage).

 

[Zack]

So how did it go?

Sorry, next weekend

 

[Magrathean]

Oh. We'll have to wait, then.

Meanwhile, comments/suggestions/corrections/questions/invitations are still welcome and appreciated.