[BioC] Regarding KEGGgraph
Marc Carlson
mcarlson at fhcrc.org
Tue Jan 12 18:20:01 CET 2010
Hi Anupam,
You can find instructions on how to update to the latest versions of R
and Bioconductor here:
http://www.bioconductor.org/docs/install/
Marc
anupam sinha wrote:
> Hi David,
> Thanks for your effort. From your session info I come to know
> that you are using KEGGgraph_1.3.2 while even after updating the BioC
> packages my KEGGgraph version is 1.1.0. Though my XML version is the latest
> one .One more thing is that I have an older version(2.4) of BioC. I have a
> couple of queries
> Can you tell me how to upgrade to the latest version of BioC and R (all my
> previous efforts have failed) ?
>
> Can you please send me the the tar ball release of the latest KEGGgraph ?
>
>
> Thanks and regards,
>
> Anupam Sinha
>
> On Tue, Jan 12, 2010 at 1:32 AM, Jitao David Zhang <davidvonpku at gmail.com>wrote:
>
>
>> Hi dear Anupam,
>>
>> I have tried the script, but I cannot replicate your error. Therefore it
>> would be helpful if you could check the version of R and KEGGgraph you use.
>> Following is my session info
>>
>>
>>> sessionInfo()
>>>
>> R version 2.11.0 Under development (unstable) (2009-11-07 r50345)
>> i686-pc-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8
>> [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grid stats graphics grDevices datasets utils methods
>> [8] base
>>
>> other attached packages:
>> [1] KEGGgraph_1.3.2 Rgraphviz_1.23.2 graph_1.25.3 XML_2.6-0
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.11.0
>>
>> The XML files could be parsed without any error.
>>
>> Best wishes,
>> David
>>
>> 2010/1/11 anupam sinha <anupam.contact at gmail.com>
>>
>> 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]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>>
>>>>> --
>>>>>
>>>>> Best wishes
>>>>> Wolfgang
>>>>>
>>>>>
>>>>> --
>>>>> Wolfgang Huber
>>>>> EMBL
>>>>> http://www.embl.de/research/units/genome_biology/huber/contact
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> 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/
>>>>
>>>>
>>>
>>> --
>>> Graduate Student,
>>> Laboratory of Computtational Biology,
>>> Centre For DNA Fingerprinting And Diagnostics,
>>> 4-1-714 to 725/2, Tuljaguda complex
>>> Mozamzahi Road, Nampally,
>>> Hyderabad-500001
>>>
>>>
>>
>> --
>> 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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