[BioC] PostForm() with KEGG

[Ovokeraye Achinike-Oduaran]

Hi Duncan,

I noticed that with the script as is, it doesn't take into
consideration the "include alias" checkbox. I tried modifying the
script to force include that option but it still did not work. Any
ideas?

u = "http://www.genome.jp/kegg-bin/search_pathway_object"
data = postForm(u,
               .params = list(org_name = "hsadd",
               unclassified = paste(readLines(file.choose()), collapse = "\n"),
               file = "", checkbox = "alias", submit = "Exec"))


Thanks again.

Avoks


On Mon, Feb 27, 2012 at 10:24 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> 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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