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
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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Try the bzfile() function instead of unz(). You'll find that you're taken to the same help page for both of those functions. ?bzfile 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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.