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")) )
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.
--
David.
Lorenzo
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