[R] Matching long strings ... was Re: Memory management in R

[Martin Morgan]

On 10/10/2010 07:11 AM, David Winsemius wrote:
> 
> On Oct 10, 2010, at 9:27 AM, Lorenzo Isella wrote:
> 
>>
>>> I already offered the Biostrings package. It provides more robust
>>> methods for string matching than does grepl. Is there a reason that you
>>> choose not to?
>>>
>>
>> Indeed that is the way I should go for and I have installed the
>> package after some struggling.
> 
> For me is was a matter of waiting. The only struggle was coming from my
> inner timer saying it was taking too long.
> 
>> Since biostring is a fairly complex package and I need only a way to
>> check if a certain string A is a subset of string B, do you know the
>> biostring functions to achieve this?
>> I see a lot of methods for biological (DNA, RNA) sequences, and they
>> may not apply to my series (which are definitely not from biology).
>> Cheers
> 
> It appeared to me that the function matchPattern should replace your
> grepl invocation that was failing. It returns a more complex structure,
> so you would need to determine what would be an exact replacement for
> grepl(...) != 1. Looks like a no-match event resutls in the start and
> end items being of length 0.
> 
>> str(  matchPattern("A", BString("BBB")) )

A couple of things from this thread.

To install a Bioconductor package follow directions here

  http://bioconductor.org/install/index.html#install-bioconductor-packages

which leads to

   source("http://bioconductor.org/biocLite.R")
   biocLite("Biostrings")

biocLite is just a wrapper around install.packages with appropriate
repositories defined.

Some Bioconductor packages are relatively mature and make relatively
advanced use of S4 classes, so looking at str() is not that helpful --
the way the user is meant to interact with the object is different from
the way the object is implemented. So the best bet is to look at the
relevant help pages

  result = matchPattern("A", BString("BBB"))
  class(result)
  class?XStringViews

and the help pages referenced there, or from which XStringViews inherits

   class("XStringViews")

and in particular

   class?Ranges

Rather than accessing the 'start' slot, use start(result). Vignettes are
used heavily in Bioconductor packages, and in particular

   browseVignettes("Biostrings")

pops up a page with several relevant vignettes, e.g., 'A short
presentation of the basic classes...' and perhaps 'Pairwise Sequence
Alignment'. These are also accessible on the Bioconductor web site,
e.g., on the pages linked from

  http://bioconductor.org/help/bioc-views/release/bioc/

The rule of thumb hinted at below -- that an operation seems to be
taking longer than it should -- probably indicates that the function is
being invoked in an inefficient way. If the documentation is opaque then
definitely the place to seek additional help is on the Bioconductor
mailing list

  http://bioconductor.org/help/mailing-list/

Hope this helps.

Martin


> Formal class 'XStringViews' [package "Biostrings"] with 7 slots
>   ..@ subject        :Formal class 'BString' [package "Biostrings"] with
> 6 slots
>   .. .. ..@ shared         :Formal class 'SharedRaw' [package "IRanges"]
> with 2 slots
>   .. .. .. .. ..@ xp                    :<externalptr>
>   .. .. .. .. ..@ .link_to_cached_object:<environment: 0x11e0e59f8>
>   .. .. ..@ offset         : int 0
>   .. .. ..@ length         : int 3
>   .. .. ..@ elementMetadata: NULL
>   .. .. ..@ elementType    : chr "ANY"
>   .. .. ..@ metadata       : list()
>   ..@ start          : int(0)
>   ..@ width          : int(0)
>   ..@ NAMES          : NULL
>   ..@ elementMetadata: NULL
>   ..@ elementType    : chr "integer"
>   ..@ metadata       : list()
> 
> Perhaps:
> 
> length(matchPattern(fut_string, past_string)@start ) == 0
> 
> You do need to use BString() on at least the past_string argument and
> maybe the fut_string as well. The BioConductor Mailing List would have a
> larger audience with experience using this package, so they should
> probably be your next avenue for advice. I am just reading the help
> pages as you should be able to do. The help page
> help("lowlevel-matching") should probably be reviewed since there may be
> efficiency issues to consider as mentioned below.
> 
> When dropped into your function with the BString coercion, it replicated
> your small example results and did not crash after a long period with
> your larger example, so I then terminated it and insert a "reporter"
> line to monitor progress. With that reporter I got up into the 200's for
> count_len without error. My laptop CPU was warming up the case and I was
> getting sleepy so I terminated the process. (I had no way of checking
> for accuracy, even if I had let it proceed, since you did not offer a
> "correct" answer.)
> 
> By the way, the construct ... grepl(. , .) != 1 ... is perhaps
> inefficient. It could more compactly be expressed as ...   !grepl(. ,
> .)  which would not be doing coercion of logicals to integers.
> 


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