You're absolutely right. I copied-pasted the code from bioperl.org onto this post without checking to see if it was wrong. When I used it in my terminal, I typed it all out and automatically changed the $ sign in $alphabet to an @, which is why it worked fine for me. And I agree, I should have gone for @bases directly instead of using that extra array which is not used anywhere else in the code. I will pay more attention to these details next time I code something up, so thanks for the tip!

On another note, I'd like to go back to my original question. I now understand that this foreach loop is being used to repeat its code (k-1) times. Let's assume $k = 3.

When $_ = 1 (first iteration of the foreach loop), we make the strings (AA, AT, AG... CC) and push them all into @newwords.

When $_ = 2, if we repeated the code inside the loop, we should produce another set of (AA...CC) and push them into @newwords, which is reinitialised in this second iteration through the loop.

I know this is not the case, however, because if I add the following code:

after this line:

we can see that we are now pushing (AAA...CCC) to the @newwords array, despite the code being exactly the same as in the first iteration.
This is exactly what I want my code to do, although I don't understand why it is working. We are pushing 3-character strings, although according to this code, we are only pushing strings of two characters ($w.$b) into the @newwords array.

Hello enderk, and welcome to the Monastery!

What you’re overlooking is the line:

@words = @newwords;
[download]

which updates the contents of @words at the end of each loop iteration. Here’s one way of visualising what is happening:

Read more... (841 Bytes)

Output:

13:20 >perl 769_SoPW.pl

BEGIN $i = 1:
  @bases = A T G C
  @words = A T G C
END   $i = 1:
  @bases = A T G C
  @words = AA AT AG AC TA TT TG TC GA GT GG GC CA CT CG CC

BEGIN $i = 2:
  @bases = A T G C
  @words = AA AT AG AC TA TT TG TC GA GT GG GC CA CT CG CC
END   $i = 2:
  @bases = A T G C
  @words = AAA AAT AAG AAC ATA ATT ATG ATC AGA AGT AGG AGC ACA ACT ACG
+ ACC TAA TAT TAG TAC TTA TTT TTG TTC TGA TGT TGG TGC TCA TCT TCG TCC 
+GAA GAT GAG GAC GTA GTT GTG GTC GGA GGT GGG GGC GCA GCT GCG GCC CAA C
+AT CAG CAC CTA CTT CTG CTC CGA CGT CGG CGC CCA CCT CCG CCC

13:20 >
[download]

As you can see, on the second iteration ($i == 2), each element of @words is initially two characters in length; so, naturally, when it is concatenated with a base character, the result is three characters long, as required.

Hope that helps,

Athanasius <°(((>< contra mundum

Iustus alius egestas vitae, eros Piratica,

Oh wow thank you so much! I did not realise @words was not being reinitialised after each iteration through the loop (which makes sense, since it was declared outside the loop).

Thanks a lot, all of you, I think I learnt a lot by trying to understand this code. Have a nice Sunday.