R问答：关于bz2文件的批量解压

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以下内容来（译）自google R-help-archive小组，仅供参考。

各位，

   

我下载了一堆bz2文件（bz2 files），我想知道能不能用R软件将这些文件以批处理的方式解压，或者一次性全部解压？

   

我试过unz()函数，效果不是很好，提示我H:/Temp/65502805_532.pair.bz2.中有一个bz2文件。谁能给点建议啊？

   

非常感谢！

   

John

以下为R程序：

> 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_UnitedStates.1252  LC_CTYPE=English_United

States.1252

[3] LC_MONETARY=English_United States.1252LC_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_1.18.0oligo_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_1.16.0splines_2.14.0        tools_2.14.0

zlibbioc_1.0.0

答一：

我说的不一定对，但我觉得unz()函数只能处理zip文件，而不能处理bz2文件。

请参考R utils包中的bunzip2()函数。

Henrik

答二：

不妨用bzfile()函数代替unz() 函数，你将进入一个针对所有这些函数的帮助页面。

   

Luke Miller

   

【问答原文】

Ask：

Hi,

   

I have downloaded abunch of bz2 files. I wonder if R will be able to unzip them in a batch mode oreven one at a time?

   

I was looking at the unzfunction. But it didn't work well. Say I have a bz2 file inH:/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_UnitedStates.1252  LC_CTYPE=English_United

States.1252

[3] LC_MONETARY=English_United States.1252LC_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_1.18.0oligo_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_1.16.0splines_2.14.0        tools_2.14.0

zlibbioc_1.0.0

Answer：

I may be wrong, but Idon't think unz() handles bz2 files - only zip files.

See bunzip2() of theR.utils package (which utilizes bzfile connections).

/Henrik

Answer：

Try the bzfile() functioninstead of unz(). You'll find that you're taken to the same help page for bothof those functions.

?bzfile

   

Luke Miller

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