[BioC] PostForm() with KEGG

[Ovokeraye Achinike-Oduaran]

Hi Duncan,

Thanks a bunch.

-Avoks

On Fri, Feb 24, 2012 at 11:09 PM, Duncan Temple Lang
<duncan at wald.ucdavis.edu> wrote:
> Hi Avoks
>
> While the form is provided by KEGG and so bio-relatd,
> you might have been better posting this to the more general r-help mailing list.
>
>
> You are posting the HTTP request to the wrong URL. That is the URL
> of the Web page that displays the form, not the URL that processes
> the input from the form.
> You have to look at the JavaScript that is referenced in the action
> attribute of the HTML form element.
>
> The second issue is that you are submitting the name of a local file.
> This won't work as is.  You either need to identify this is the name of a file and not the contents
> of the file to send, or else send the contents.  In this form, you can send the
> contents via the the unclassified parameter.
>
>
> u = "http://www.genome.jp/kegg-bin/search_pathway_object"
> data = postForm(u,
>                .params = list(org_name = "hsadd",
>                               unclassified = "hsa:7167 hsa:GPI cpd:C00118\nALDOA 1.2.1.12 C00236",
>                               file = "", submit = "Exec"))
>
>
> If your input is in a file, you can use
>
>  unclassified = paste(readLines(file.choose()), collapse = "\n")
>
> as the value for the unclassified parameter.
>
>
> There are additional parameters that the form accepts that may be relevant for your search.
>
>
> As for processing the results, you will want to use
>
>  doc = htmlParse(data, asText = TRUE)
>
> and then use getNodeSet()/xpathSApply() or direct tree extraction to access the nodes you want, e.g.
>
>  xpathSApply(doc, "//li/a",  xmlGetAttr, "href")
>
>
>  D.
>
>
> On 2/24/12 6:09 AM, Ovokeraye Achinike-Oduaran wrote:
>> Hi all,
>>
>> I am trying to use postForm() with the KEGG website but I am stuck on
>> how to get my results. Is it possible (code below) or am I using
>> postForm() wrongly? The code appears to run but I'm not quite sure how
>> to read the results assuming there are any. Please help.
>>
>> Thanks.
>>
>> Avoks
>> ____
>>
>> data = postForm("http://www.genome.jp/kegg/tool/map_pathway1.html",
>> org_name = "hsadd",
>> file = file.choose(),
>> submit = "Exec")
>>
>>> sessionInfo()
>> R version 2.14.1 (2011-12-22)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_xxx.1252  LC_CTYPE=English_xxx.1252
>> [3] LC_MONETARY=English_xxx.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_xxx.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] RHTMLForms_0.5-1 XML_3.9-4.1      RCurl_1.91-1.1   bitops_1.0-4.1
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.14.1
>>
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>
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