Downloading and extracting .gz data file using R

Question

I already tried to solve my problem by adaption of this similar question. However, I get the following error for the URL or the file I want to do this with.

trying URL 'http://cbio.mskcc.org/microrna_data/human_predictions_S_C_aug2010.txt.gz'
Content type 'application/x-gzip' length 65933953 bytes (62.9 Mb)
opened URL
downloaded 62.9 Mb

 Show Traceback

 Rerun with Debug
 Error in open.connection(file, "rt") : cannot open the connection In addition: Warning message:
In open.connection(file, "rt") :
  cannot open zip file 'D:....' 

here is what I tried:

url_S_C <- "http://cbio.mskcc.org/microrna_data/human_predictions_S_C_aug2010.txt.gz"
tmpFile <- tempfile()
fileName <- gsub(".gz","",basename(url_S_C))
download.file(url_S_C, tmpFile)
data <- read.table(unz(tmpFile, fileName))
unlink(tmpFile)

Maybe someoe here can help me why this particular file is not working for me? Please note, that this file is quiet large (62.9 Mb), but I was not able to reproduce the error with the URL from the similar question.

Thank you!

Answer 1

Some additional options, with base R:

url <- "http://cbio.mskcc.org/microrna_data/human_predictions_S_C_aug2010.txt.gz"
tmp <- tempfile()
##
download.file(url,tmp)
##
data <- read.csv(
  gzfile(tmp),
  sep="\t",
  header=TRUE,
  stringsAsFactors=FALSE)
names(data)[1] <- sub("X\\.","",names(data)[1])
##
R> head(data)
   mirbase_acc mirna_name gene_id gene_symbol transcript_id ext_transcript_id           mirna_alignment
1 MIMAT0000062 hsa-let-7a    5270    SERPINE2    uc002vnu.2         NM_006216   uuGAUAUGUUGGAUGAU-GGAGu
2 MIMAT0000062 hsa-let-7a  494188      FBXO47    uc002hrc.2      NM_001008777 uugaUA-UGUU--GGAUGAUGGAGu
3 MIMAT0000062 hsa-let-7a   80025       PANK2    uc002wkc.2         NM_153638   uugauaUGUUGG-AUGAUGGAgu
4 MIMAT0000062 hsa-let-7a   26036      ZNF451    uc003pdp.2          AK027074    uuGAUAUGUUGGAUGAUGGAGu
5 MIMAT0000062 hsa-let-7a     586       BCAT1    uc001rgd.3         NM_005504    uugaUAUGUUGGAUGAUGGAGu
6 MIMAT0000062 hsa-let-7a   22903       BTBD3    uc002wnz.2         NM_014962  uuGAUAUGUUGGAU-GAUGG-AGu
                  alignment            gene_alignment mirna_start mirna_end gene_start gene_end
1     | :|: ||:|| ||| ||||    aaCGGUGAAAUCU-CUAGCCUCu           2        21        495      516
2     || |||:  ::||||||||:  acaaAUCACAGUUUUUACUACCUUc           2        19        459      483
3         |::||: ||||||||     aauuucAUGACUGUACUACCUga           3        17         77       99
4      || || |   | |||||||     ccCUCUAGA---UUCUACCUCa           2        21       1282     1300
5        :|| |:   ||||||||     guagGUAAAGGAAACUACCUCa           2        19       6410     6431
6    || || ||| || ||||| ||   uaCUUUAAAACAUAUCUACCAUCu           2        21       2265     2288
              genome_coordinates conservation align_score seed_cat energy mirsvr_score
1 [hg19:2:224840068-224840089:-]       0.5684         122        0 -14.73      -0.7269
2  [hg19:17:37092945-37092969:-]       0.6464         140        0 -16.38      -0.1156
3    [hg19:20:3904018-3904040:+]       0.6522         139        0 -16.04      -0.2066
4   [hg19:6:56966300-56966318:+]       0.7627         144        7 -14.51      -0.8609
5  [hg19:12:24964511-24964532:-]       0.6775         150        7 -15.09      -0.2735
6  [hg19:20:11906579-11906602:+]       0.5740         131        0 -12.59      -0.2540

---

Or if you are on a Unix-like system, you could obtain the .txt file (either outside of R or using system or system2 from within R) like this:

[nathan@nrussell tmp]$ url="http://cbio.mskcc.org/microrna_data/human_predictions_S_C_aug2010.txt.gz"
[nathan@nrussell tmp]$ wget "$url" && gunzip human_predictions_S_C_aug2010.txt.gz

and then proceed as above, where you are reading in human_predictions_S_C_aug2010.txt from wherever wget and gunzip were executed,

data <- read.csv(
  "~/tmp/human_predictions_S_C_aug2010.txt",
  stringsAsFactors=FALSE,
  header=TRUE,
  sep="\t")

in my case.