Question: Regarding KEGGgraph
0
gravatar for anupam sinha
10.0 years ago by
anupam sinha270
anupam sinha270 wrote:
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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]]
pathways network process • 682 views
ADD COMMENTlink modified 10.0 years ago by Wolfgang Huber13k • written 10.0 years ago by anupam sinha270
Answer: Regarding KEGGgraph
0
gravatar for Wolfgang Huber
10.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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_FILE S/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_IDEN TIFICATION=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
ADD COMMENTlink written 10.0 years ago by Wolfgang Huber13k
@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@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_FIL ES/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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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@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@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/ [[alternative HTML version deleted]]
ADD REPLYlink written 10.0 years ago by Jitao David Zhang340
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_FI LES/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=e n_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_ID ENTIFICATION=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
ADD REPLYlink written 10.0 years ago by anupam sinha270
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@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@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@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_F ILES/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_I DENTIFICATION=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@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@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/ [[alternative HTML version deleted]]
ADD REPLYlink written 10.0 years ago by Jitao David Zhang340
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@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@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@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@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@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@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/ > -- 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 [[alternative HTML version deleted]]
ADD REPLYlink written 10.0 years ago by anupam sinha270
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_COLLAT E=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/ >> >> > > > >
ADD REPLYlink written 10.0 years ago by Marc Carlson7.2k
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