I'm going to be doing some non-linear regression (with a huge and messy residual function), and I am thinking of using PDL::Fit::LM (I had some trouble getting Levmar to install).
The explanatory variables for my fit are DNA sequence (which I'm feeding into a position-specific weight-matrix). What's the easiest way to put a DNA sequence into a piddle? Given that the function i'm working with is a big mess, performance is a consideration.
Since my weight-matrix is constrained so that the sum of weights at a given position comes to zero, my plan is currently to represent each nucleotide as a vector of three elements A -> [1,0,0], C -> [0,1,0], G -> [0,0,1], T -> [-1,-1,-1]. This way I can take a subsequence of my total sequence and just multiply it with my weight-matrix and get the score.
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Flies •
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If I did understand your question correctly you want to store the nucleotide sequence in a PDL data structure, is that correct? If not, then please update your question, it is a bit confusing. I do not immediately see the advantage of doing this, instead of sticking with a normal string. The question is then, why would you want to do this? Anyway, you could eventually use PDL::Char
something along the lines
use PDL;
use PDL::Char;
my $pchar = PDL::Char->new( ['ACGT', 'ATGT', 'TGAA']);
As you don't have control over the storage size of a variable (could think of using a 2bit encoded format, but there is no bit-pdl) this might already be the most efficient way meomory-wise.
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+1 for the most amusing BioStar title to date.
What's your question? Seems like you've answered it yourself.
Others have successfully used PDL for encoding alignments and other DNA related stuff. Too bad the PDL documentation terrible
@qdjm I'm just guessing that I'm not the first person to do this, and I'm wondering what solutions people have come up with. I mention my current idea as a point of reference.