Hi Florian,
I just removed the 'substitutionArray' slot from PairwiseAlignments
objects in Biostrings 2.27.7. The slot didn't seem to be used/needed
by any downstream method.
> packageVersion("Biostrings")
[1] ‘2.27.7’
> x <- "xxxabcdefghijklmnopqyyy"
> y <- "abcdhijkzzzzlmnpqr"
> pa <- pairwiseAlignment(x, y)
> slotNames(pa)
[1] "pattern" "subject" "type" "score"
"gapOpening"
[6] "gapExtension"
> validObject(pa)
[1] TRUE
> object.size(pa)
35528 bytes
... instead of 35308996 bytes! 3 orders of magnitude smaller :-)
Cheers,
H.
On 11/05/2012 03:45 AM, Hahne, Florian wrote:
Indeed. I did not look the far into the implementation, it just seemed odd
to me that the objects got that inflated. scoreOnly is not really that
helpful if you want to deal with the actual alignments. The only
reasonable application I see for it is if you want to rank a bunch of
sequences by pairwise similarity. This gigantic memory footprint is really
breaking things once you start doing a lot of these pairwise alignment
operations in parallel. mclapply complains about not being able to turn
such large objects into a raw vector, and serializing to disk quickly
fills your hard drive. You also loose a lot of the time gained by parallel
processing just by writing and loading gigabytes of data...
I don't know enough about the internals of the PairwiseAlignments classes,
but it seems that there must be a way to avoid having this huge array as
part of the object. As a quick and dirty fix for now I just replaced the
substitutionArray slot with an empty matrix and all the downstream
operations that I wanted to do still work. Would be great if you could
take a look into this, Herve.
Thanks,
Florian
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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