[R] how to unzip files in R

[ql16717]

Hi Henrik,

That is exactly what I was looking for. I worked great. Many thanks.

By the way it doesn't seem to be able to do batch mode. I guess I will
have to iterate through. But thats ok.

John

On 1/31/12, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
> I may be wrong, but I don't think unz() handles bz2 files - only zip files.
>
> See bunzip2() of the R.utils package (which utilizes bzfile connections).
>
> /Henrik
>
>
> On Tue, Jan 31, 2012 at 2:34 PM, ql16717 <ql16717 at gmail.com> wrote:
>> Hi,
>>
>> I have downloaded a bunch of bz2 files. I wonder if R will be able to
>> unzip them in a batch mode or even one at a time?
>>
>> I was looking at the unz function. But it didn't work well. Say I have
>> a bz2 file in H:/Temp/65502805_532.pair.bz2. Anyone has any
>> suggestion?
>>
>> thanks
>> John
>>
>>> setwd("H:\\Temp\\")
>>> getwd()
>> [1] "H:/Temp"
>>> fn<-list.files(pattern="bz2", full.names=TRUE)
>>> fn
>> [1] "./65502805_532.pair.bz2"
>>> unz(description=fn, filename="65502805_532.pair", open="r")
>> Error in unz(description = fn, filename = "65502805_532.pair", open = "r")
>> :
>>  cannot open the connection
>> In addition: Warning message:
>> In unz(description = fn, filename = "65502805_532.pair", open = "r") :
>>  cannot open zip file './65502805_532.pair.bz2'
>>
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] pdInfoBuilder_1.18.0 oligo_1.18.1         oligoClasses_1.16.0
>> affxparser_1.26.2    RSQLite_0.10.0
>> [6] DBI_0.2-5            Biobase_2.12.1
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.22.0         Biostrings_2.22.0     bit_1.1-8
>> ff_2.2-4              IRanges_1.12.1
>> [6] preprocessCore_1.16.0 splines_2.14.0        tools_2.14.0
>> zlibbioc_1.0.0
>>
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>