[BioC] gpr.gz

[Sean Davis]

On 10/13/05 2:50 PM, "Rafael A. Irizarry" <ririzarr at jhsph.edu> wrote:

> but then how to create an RGlist or marrayRaw? do i have to
> rewrite or hack the gpr parsers?
> 
> On Thu, 13 Oct 2005, Sean Davis wrote:
> 
>> On 10/13/05 2:39 PM, "Rafael A. Irizarry" <ririzarr at jhsph.edu> 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.
>> 
>> Rafael,
>> 
>> Look at ?gzfile.  Will that do what you want?
>> 
>> Txtfile <- readLines(gzfile('txtfile.gz'))
>> 
>> Sean
>> 
> 

Rafael,

I think that would be the case, yes.  I haven't tried it, but I think you
might be able to get away with modifying only three lines in the readGAL
function (noted below).  I may have missed some and I haven't tested, but I
think these should work.

galfile <- dir(path = path, pattern = "\\.gal$")
galfile <- dir(path = path, pattern = "\\.gal.gz$")


chunk <- readLines(galfile, n = 100)
chunk <- readLines(gzfile(galfile), n = 100)


gal <- read.table(galfile, header = header, sep = sep, quote = quote,
        skip = skip, as.is = as.is, comment.char = "", ...)

gal <- read.table(gzfile(galfile), header = header, sep = sep,
    quote = quote, 
        skip = skip, as.is = as.is, comment.char = "", ...)

Sean