On Oct 10, 2010, at 11:35 AM, Martin Morgan wrote:
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
The above was the most surprising example for me (not being
particularly S4-savvy). Looks like it parses as:
`?`(class, XStringViews)
Is that an S4 sort of extension for accessing documentation or have I
just missed a more general method? I tried looking at the help Index
for the "methods" package.
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.
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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