On Mon, May 12, 2014 at 11:41 AM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> Hi Michael,
>
>
> On 05/09/2014 04:39 PM, Michael Lawrence wrote:
>
>> What would be the fastest way to do this with a DNAString? Just an
>> alphabetFrequency?
>>
>
> That would do it.
>
> A couple of other issues I ran into with the 2bit code:
>
> (1) It fails on empty sequences:
>
> > export(DNAStringSet(c("AA", "", "CC")), "ww.2bit")
> Warning message:
> In (function (object, seqname) :
> needLargeMem: trying to allocate 0 bytes (limit: 17179869184)
> Error in sapply(object, function(x) typeof(x) == "externalptr" &&
> is(x, :
> error in evaluating the argument 'X' in selecting a method for
> function 'sapply': Error in (function (object, seqname) : UCSC
> library operation failed
>
>
Thanks for catching this one.
> (2) Could be that internal helper rtracklayer:::.DNAString_to_twoBit()
> is introducing a memory leak as it doesn't seem that the memory
> the returned external pointer is pointing to (a struct twoBit) is
> ever released. The memory leak is minor if the sequence passed via
> 'object' has no masks but can be important if there are masks and
> if the masks are made of hundreds of thousands of ranges.
>
>
Right now it is the responsibility of the caller to free that memory.
Probably should have used a finalizer on the externalptr, but the way it
works now is that the write function frees the object. So it's not leaking
(as far as I know), but the design could be improved.
> Thanks,
> H.
>
>
>>
>> On Fri, May 9, 2014 at 4:07 PM, Hervé Pagès <hpa...@fhcrc.org
>> <mailto:hpa...@fhcrc.org>> wrote:
>>
>> Hi Michael,
>>
>> library(rtracklayer)
>> library(Biostrings)
>> x <- DNAStringSet("AAA-CCC-GGG-TTT-__NNN-KKK")
>>
>>
>> Then:
>>
>> > x
>> A DNAStringSet instance of length 1
>> width seq
>> [1] 23 AAA-CCC-GGG-TTT-NNN-KKK
>>
>> > export(x, "x.2bit")
>>
>> > import("x.2bit")
>> A DNAStringSet instance of length 1
>> width seq names
>> [1] 23 AAATCCCTGGGTTTTTNNNTTTT 1
>>
>> What about having the "export" method for TwoBitFile raise an error
>> (or at least issue a warning) instead of silently turning everything
>> that is not A, C, G, T, or N into a T?
>>
>> Thanks,
>> H.
>>
>> --
>> 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 <mailto:hpa...@fhcrc.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>> _________________________________________________
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>>
>>
>>
> --
> 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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