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regexpr and portability issue

3 messages · Marco Blanchette, Gabor Grothendieck, Brian Ripley

Original
Marco Blanchette
# 
Dear all--

I am still forging my first arms with R and I am fighting with regexpr() as
well as portability between unix and windoz. I need to extract barcodes from
filenames (which are located between a double and single underscore) as well
as the directory where the filename is residing. Here is the solution I came
to:

aFileName <- 
"/Users/marco/Desktop/diagnosticAnalysis/test/MA__251329410021_S01_A01.txt"
t <- regexpr("__\\d*_",aFileName, perl=T)
t.dir <- regexpr("^.*/", aFileName, perl=T)
base.name <- substr(aFileName, t+2, t-2 + attr(t,"match.length"))
base.dir <- substr(aFileName, t.dir, attr(t.dir,"match.length"))

My questions are:
1) Is there a more elegant way to deal with regular expressions (read here:
more easier, more like perl style).
2) I have a portability problem when I extract the base.dir Windoz is using
'\' instead of '/' to separate directories.

Any suggestions/comments

Many Tx

Marco Blanchette, Ph.D.

mblanche at uclink.berkeley.edu

Donald C. Rio's lab
Department of Molecular and Cell Biology
16 Barker Hall
University of California
Berkeley, CA 94720-3204

Tel: (510) 642-1084
Cell: (510) 847-0996
Fax: (510) 642-6062
Gabor Grothendieck
# 
Try this.  The regular expression says to match 
- anything 
- followed by a double underscore 
- followed by one or more digits
- followed by an underscore 
- followed by anything.  
The digits have been parenthesized so that they can be referred to in
the backreference "\\1".    Also use the R function dirname
rather than regular expressions.

base.name <- sub(".*__([[:digit:]]+)_.*", "\\1", aFileName, ext = TRUE)
base.dir <- dirname(aFileName)
On 8/3/05, Marco Blanchette <mblanche at uclink.berkeley.edu> wrote:
Brian Ripley
#
On Tue, 2 Aug 2005, Marco Blanchette wrote:

            

      
      
      
    

        
Yes, use sub and backreferences.  An example from the R sources doing 
something similar:

             wfile <- sub("/chm/([^/]*)$", "", file)
             thispkg <- sub(".*/([^/]*)/chm/([^/]*)$", "\\1", file)

However, R does have functions basename() and dirname() to do this!

            

      
      
      
    

        
That is misinformation: Windows (sic) accepts either / or \ (see the 
rw-FAQ and the R FAQ).  Use chartr("\\", "/", path) to map \ to /.

The `portability problem' appears to be of your own making -- take heart 
that R itself manages to manipulate filepaths portably.