[BioC] gpr.gz

Henrik Bengtsson hb at maths.lth.se
Fri Oct 14 00:25:11 CEST 2005

FYI: I had some problems with GPR files, read.table, and an gzfile when 
I tried this out two years ago in aroma.  I cannot remember what the 
exact problem was (some kind of read.table error), but I ended up 
gunzipping to temporary file in my parser/reader.  My code is now doing

   if (regexpr("[.]gz$", filename) != -1) {
     tmpname <- tempfile();
     n <- gunzip(filename, tmpname);
     filename <- tmpname;

gunzip() is simply a function that reads a gzfile and writes to a 
regular file connection.  Less efficient for now, but at least you can 
keep you files gzipped.  The read.table problem might been fixed now, I 
haven't tried.


Rafael A. Irizarry wrote:
> yes, but then i need to hack the existing parsers. maybe instead of just 
> me doing it, the maintainer(s) can do it for everybody? see Sean's email 
> for what he suggests.
> -r
> On Thu, 13 Oct 2005, Robert Gentleman wrote:
>>  Does gzfile not do what you want?
>>  > apropos("gz")
>>[1] "gzcon"  "gzfile"
>>Rafael A. Irizarry wrote:
>>>hi! any recs on how to deal with gzipped gpr files? if possible id like to 
>>>read them into bioc without unzipping them first. 
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
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