[BioC] [R] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?

[Gabor Grothendieck]

I will send you offline an enhancement for read.xls that accepts
ftp connections.

On Sun, Jul 26, 2009 at 11:32 AM, <mauede at alice.it> wrote:
> It works if the web file adress is of the type:  "http://".
> It does not work if the web file adress is of the type:  "'ftp://".
>> outFile <- read.xls("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls")
> Error in xls2csv(xls, sheet, verbose = verbose, ..., perl = perl) :
>  Unable to read xls file 'ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls'.
> Error in file.exists(tfn) : invalid 'file' argument
>
> But the file does exists as shown in the following:
>> download.file("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls","outFile")
> trying URL 'ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls'
> ftp data connection made, file length 2563072 bytes
> opened URL
> downloaded 2.4 Mb
>
> Can the two steps (download + read.xls) be performed with one command line  only ?
>
> Thank you,
> Maura
>
>
>
> -----Messaggio originale-----
> Da: r-help-bounces at r-project.org per conto di Daniel Nordlund
> Inviato: lun 06/07/2009 20.45
> A: r-help at stat.math.ethz.ch
> Oggetto: Re: [R] R: R: Is there a way to extract some fields data fromHTML      pages through any R function ?
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org
>> [mailto:r-help-bounces at r-project.org] On Behalf Of mauede at alice.it
>> Sent: Sunday, July 05, 2009 11:28 PM
>> To: Martin Morgan
>> Cc: r-help at stat.math.ethz.ch
>> Subject: [R] R: R: Is there a way to extract some fields data
>> from HTML pages through any R function ?
>>
>> It helps. But it is overly sophisticated.
>> I have already downloaded and used the Excel file containing
>> the validated stuff.
>>
>> Since there are R commands to download gzip as well as FASTA
>> files, I wonder whether it is possible to
>> automatically download the Excel file from
>> http://mirecords.umn.edu/miRecords/download.php
>> Actually the latter may not be the actual file URL because it
>> is necessary to click on the word "here" to download the file.
>>
>> Thank you,
>> Maura
>>
> Maura,
>
> I haven't seen a response to your question (however, I just may have missed
> it, or you mave have received an off-line response).  I went to the URL
> above and found that the Excel file is at
>
> http://mirecords.umn.edu/miRecords/download_data.php?v=1
>
> I think you could use the read.xls() function from the gdata package to get
> the file, something like this
>
> library(gdata)
> df <- read.xls("http://mirecords.umn.edu/miRecords/download_data.php?v=1")
>
> Hope this is helpful,
>
> Dan
>
> Daniel Nordlund
> Bothell, WA USA
>
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