New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

read compressed files from a URL #163

Closed
katwre opened this Issue May 4, 2015 · 2 comments

Comments

Projects
None yet
3 participants
@katwre

katwre commented May 4, 2015

Here is an example with an error:

l <- "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/wgEncodeHaibMethylRrbsImr90UwSitesRep1.bed.gz"
d <- read_delim(l, delim="\t")
Error in collectorsGuess(source, tokenizer, n = 100) : 
  embedded nul in string: '\x89\032\xc7\003\f\xc4#}\xe8\xda\xf5\xbb\x80\xf1\0\023ēo\026O\xe4#\x98Ч\x92\b\xe3\021L\xe4\xf3\xb0\x88\xe3A\006|\xce7澯\xb6n\xeaT\xea\xce\xe7]\\\030\xea|\xb2>$7\xb4\xeb9\xb1ʺ\xf0\xf9u\xa1\031\xd7,~\xbe\177&\xbc\xca\xc5\xea\016\xbd\004t\xbe\x82\xef\xbfR\x8fY_Y\xfa\xfd\xaa\\Ot\x8dH\xc0\x97\xfd\xbb\xbe\027l\xea\xbb\177\xd5Ýw\xa6\v\xe2|K\xbf\xe4\xe7\xd8<\xf9\xad\xeb\x93;Uu\xcbh\003\xf9\xd94\022\x9f\x8b\x95ɦ\037\027\xf2\xbd\xde;\xa7\xa7\xb0\xd2qm3C\xf1\xe7\003\xbf\037#\xed}X\xbd\xb1\x97\xa0b\xaf\xc4J?V\xe8\x85T\xe8U\xf8/\026]\x93I\xeb6\032\x8a?'Iy\xb5\x97U\x8a\xbd\004\025{eV\xe5\017/\xa4B\xaf\xce\177Q\x97Ð]\002\xf2j\001;\x89\x94\xae\xb1AT\x82\xe2\xd7\xe7#\032\x9a\xe5\xe7e\025\x86%\xa1 \xac\x91D\xca|\x84\177]\xc8\xfb\x80Τ\xc2\xca\177\025'
@maehler

This comment has been minimized.

maehler commented Jun 11, 2015

I just experienced the same issue:

> read_tsv("ftp://plantgenie.org/Data/PopGenIE/Populus_tremula/v1.0/Annotation/Potra01_GO.tsv.gz")
Error in collectorsGuess(source, tokenizer, n = 100) : 
  embedded nul in string: '\f\xcc\xfa\xb2Q\x9b\0g\024\xfb\xeam\a\xb1_*\x9f\x89P\017\xa7\xa4\xf2\031O\0\xbcP'

If I download the file first it works fine.

@npjc

This comment has been minimized.

Contributor

npjc commented Jun 18, 2015

And another...

read_* lets you read in a .gz file and also lets you download a file from a url.

It does not however decompress a file downloaded from a url:

a_url <- "ftp://data.modencode.org/D.melanogaster/Histone-Modification/ChIP-chip/computed-peaks_gff3/H3K9acS10P%3aCell-Line=S2-DRSC%23Developmental-Stage=Late-Embryonic-stage%23Tissue=Embryo-derived-cell-line%3aChIP-chip%3aRep-1%3a%3aDmel_r5.32%3amodENCODE_2660.gff3.gz"

readr::read_tsv(a_url, skip = 100)
#> Error in collectorsGuess(source, tokenizer, n = 100) : 
#>   embedded nul in string: '\x91\xff\xa9\017b\xac\036\x823\xf2~\xd0\025^\xec\xe5\xc9!\005\x8d\0\032\xb5=R~\xf0]\xf4\020\x9c\xb1\xf8]3y\xa1\x98\xd7L\xa7\xc9J4E\xf1\xf7\xbe\x8fB\xf5\020\x9cQ\xafo]&\xbc@v\xc4\xc5Ljd`>F\xaa\xf7Y\xfd\036\x823\x9a\xf2h\xea.e\xb1\x9b\x91\xc7' 

(if you download the file and read_tsv it in from disk all is well).

I would have expected that download+decompress. If this is possible it would be great!

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.