Entering edit mode
Fraser Sim
▴
270
@fraser-sim-3567
Last seen 10.1 years ago
Hi David,
Thanks. That doesn?t solve the problem though, try to get the KEGG
pathway
?hsa03010? using
>getCategoryIndepKGMLurl(?03010?,organism = ?hsa?)
It doesn?t produce a valid html link. It should find
?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non-
metabolic/organisms/hsa/hsa03010.
xml? which is correct but because 'getKGMLurl' returns the invalid
?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa
03010.
xml?, it then returns
?ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/hsa/hsa0301
0.xml?
which does not exist.
Note the substitution of "_" with "-". I?m pretty sure it?s a bug in
getKGMLurl.
Thanks,
Fraser
From: Jitao David Zhang [mailto:davidvonpku@gmail.com]
Sent: Monday, November 23, 2009 5:58 AM
To: Fraser Sim
Cc: bioc
Subject: Re: [BioC] KEGGgraph bug
Hi Fraser,
? Thanks for the reporting.? The reason for this is that since April
2009
the KEGG server saves the non-metabolic and metabolic pathways in two
different sub-directory separatedly, and so far as I know there is no
way to
tell whether the pathway is metabolic alone from the pathway id.
Therefore
'getKGMLurl' can NOT garantee to return the correct address. However,
'retrieveKGML' tries both metabolic and non-metabolic pathway
directories,
therefore it is able to download the file remotely.
? To retrieve the URL for a pathway, use 'getCategoryIndepKGMLurl'
function,
which tries both non-metabolic and metabolic directories. 'getKGMLurl'
will
be hidden from the next release.
? I hope my answer solves your question.
? Best wishes,
David
2009/11/20 Fraser Sim <fjsim at="" buffalo.edu="">
I have found a problem with how 'getKGMLurl' constructs the URL for
retrieving the KGML files. It looks like the '_' should be '-' in
non_metabolic portion of the generated url. I am using the current
release
versions, R2.10.0 and KEGGgraph 1.2.0.
Thanks,
Fraser
> library(KEGGgraph)
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
? ? ? ?The following object(s) are masked from package:XML :
? ? ? ? addNode
Loading required package: Rgraphviz
Loading required package: grid
> url <- getKGMLurl('04330', organism = "hsa")
> url
[1]
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa
04330.
xml"
> parseKGML(url)
failed to load external entity
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa
04330.
xml"
Error: 1: failed to load external entity
"ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa
04330.
xml"
> parseKGML(gsub("_","-",url))
KEGG Pathway
[ Title ]: Notch signaling pathway
[ Name ]: path:hsa04330
[ Organism ]: hsa
[ Number ] :04330
[ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png
[ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330
------------------------------------------------------------
Statistics:
? ? ? ?30 node(s)
? ? ? ?16 edge(s)
? ? ? ?0 reaction(s)
------------------------------------------------------------
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United
States.1252 ? ?LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United
States.1252
attached base packages:
[1] grid ? ? ?stats ? ? graphics ?grDevices datasets ?utils ? ?
methods
base
other attached packages:
[1] KEGGgraph_1.2.0 ?Rgraphviz_1.24.0 graph_1.24.0 ? ? XML_2.6-0
rcom_2.2-1 ? ? ? rscproxy_1.3-1
loaded via a namespace (and not attached):
[1] tools_2.10.0
>
_______________________________________________
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/