Re^2: Create the reverse complement DNA sequence without pattern matching and reverse built-in function?

I tried to alert the OP to this issue in my post:

I would expect this to be tremendously slower than using tr/// on large data sets.

And your benchmark confirms it; there's a tremendous difference, in favor of using tr/// to do what it was designed to do. I think your tr/// method missed reversing the string afterwards, but that won't change the fact that the tr/// approach is the way to go.

Dave

Comment on Re^2: Create the reverse complement DNA sequence without pattern matching and reverse built-in function? Select or Download Code

Replies are listed 'Best First'.
Re^3: Create the reverse complement DNA sequence without pattern matching and reverse built-in function? by BrowserUk (Patriarch) on Feb 19, 2014 at 19:07 UTC
I tried to alert the OP to this issue in my post: Sorry. I missed that. your tr/// method missed reversing the string afterwards, but that won't change the fact that the tr/// approach is the way to go. Right on both counts. And it make's more of a difference than I was expecting, but still 80x faster than the next best: `tr => q[ ( my $revcmp = reverse $seq ) =~ tr[ACGTacgt][tgcaTGCA]; ], C:\test>junk60 Rate hdb atcroft davido tr hdb 9827/s -- -36% -71% -100% atcroft 15292/s 56% -- -55% -99% davido 33822/s 244% 121% -- -99% tr 2640400/s 26770% 17167% 7707% --` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply] [d/l]

Replies are listed 'Best First'.

Re^3: Create the reverse complement DNA sequence without pattern matching and reverse built-in function?
by BrowserUk (Patriarch) on Feb 19, 2014 at 19:07 UTC

I tried to alert the OP to this issue in my post:

Sorry. I missed that.

your tr/// method missed reversing the string afterwards, but that won't change the fact that the tr/// approach is the way to go.

Right on both counts. And it make's more of a difference than I was expecting, but still 80x faster than the next best:

    tr => q[
        ( my $revcmp = reverse $seq ) =~ tr[ACGTacgt][tgcaTGCA];
    ],

C:\test>junk60
             Rate     hdb atcroft  davido      tr
hdb        9827/s      --    -36%    -71%   -100%
atcroft   15292/s     56%      --    -55%    -99%
davido    33822/s    244%    121%      --    -99%
tr      2640400/s  26770%  17167%   7707%      --
[download]

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

[reply]
[d/l]