[BioC] Regarding KEGGgraph

[anupam sinha]

Hi David and Wolfgang,
                                    Thanks a lot for our suggestions. I
updated the packages (both R and Bioconductor). But still the same error
message.Apologies for not stating my problem clearly and this time I will
provide the files . I will have another go at it. I have this folder by name
ORG_XML_FILES  where I need to run my R script. This folder contains
directories for organisms which in turn contain the pathways in KGML format.
So I start from ORG_XML_FILES directory and decend into each of the
individual subdirectory (having KGML files of a specific organism). Read all
these KGML files to a list and construct a metabolic network. Next step is
to come out of this subdirectory into ORG_XML_FILES and then descend into
next subdirectory repeat the operation. I have written a script for it and
it doesn't seem to be working. Gives error:

Error in UseMethod("xmlAttrs", node) :
 no applicable method for "xmlAttrs"

I am forwarding three files. Two of the files are the zipped folders of
pathways of organisms (KGML format).
Third is my script.

*aac is the KEGG organism identifier for Alicyclobacillus acidocaldarius
aae is the KEGG organism identifier for Aquifex aeolicus
*
Apologies if the mail is bit long.

Regards,

Anupam


On Mon, Jan 11, 2010 at 2:33 AM, Jitao David Zhang <davidvonpku at gmail.com>wrote:

> @Wolfgang: Thank you very much for the good tip!
>
> Hi dear Anupam,
>
>   Exactly, Wolfgang made the point. It is a known issue related to the old
> XML package, and has been long solved since the version 1.1.x. Please
> therefore update R, Bioconductor and KEGGgraph.
>
>   Best wishes,
> David
>
>
> 2010/1/10 Wolfgang Huber <whuber at embl.de>
>
> Dear Anupam
>>
>> the first thing you should try is upgrading to the most recent version of
>> R and Bioconductor.
>>
>> Next, if that does not help, please provide a reproducible example (others
>> cannot see the files in your /home/anupam/ directory and hence not reproduce
>> your problem, which almost always is a prerequisite for providing help).
>>
>>        Best wishes
>>        Wolfgang
>>
>>
>>  Hi all,
>>>         I have downloaded the KGML files of for all the pathways of some
>>> organisms . I want to automate the process of constructing the metabolic
>>> networks of these organisms. In a directory by name ORG_XML_FILES I have
>>> the
>>> following directories and  files
>>>
>>> /aac(dir)       /aae(dir)          etc ......
>>> 1.xml           4.xml
>>> 2.xml           5.xml
>>> 3.xml           6.xml
>>>
>>> I want to enter each subdirectory (for e.g. aac) read all the xml files
>>> and
>>> construct a metabolic network using KEGGgraph
>>>
>>> I have written the following script:
>>>
>>> setwd("/home/anupam/Research/Anupam_data/ORG_XML_FILES/")
>>>  list.files()->org_xml_dirs
>>>  for (i in org_xml_dirs){
>>>  setwd(file.path("/home/anupam/Research/Anupam_data/ORG_XML_FILES/",i))
>>>  org_xml<-list.files()
>>>  for(j in org_xml)
>>>  {
>>>  graph_list<-pairlist()
>>>  graph<-parseKGML2Graph(j,genesOnly=TRUE)
>>>  graph_list<-c(graph_list,list(graph))
>>>  }
>>>  org_met_net<-mergeKEGGgraphs(graph_list)
>>>  met_org<-igraph.from.graphNEL(org_met_net,name=TRUE)
>>>
>>>  write.graph(met_org,"/home/anupam/Research/Anupam_data/ORG_XML_FILES/i.metnet",format=c("NCOL"))
>>>  }
>>>
>>> But it is giving the following error :
>>>
>>> Error in UseMethod("xmlAttrs", node) :
>>>  no applicable method for "xmlAttrs"
>>>
>>>
>>> here's my sessioninfo.
>>>
>>>  sessionInfo()
>>>>
>>> R version 2.9.0 (2009-04-17)
>>> x86_64-redhat-linux-gnu
>>>
>>> locale:
>>>
>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] KEGGgraph_1.1.0 graph_1.22.2    XML_2.5-1       igraph_0.5.2-2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.9.0
>>>
>>>
>>> Can anyone help me out with this ? thanks in advance.
>>>
>>> Regards,
>>>
>>> Anupam
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
>> --
>>
>> Best wishes
>>     Wolfgang
>>
>>
>> --
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber/contact
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> Jitao David Zhang
> Biological Statistics and Computational Biology Ph.D.
> Division of Molecular Genome Analysis
> DKFZ, Heidelberg D-69120, Germany
>
> http://www.NextBioMotif.com/
>



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