[BioC] Using \'SSOAP\' to do EMBL-EBI Web Services of emboss needle

LiGang [guest] guest at bioconductor.org
Mon Sep 24 10:42:38 CEST 2012

hello everyone:

I want to use SSOAP package to do some web service of EMBL-EBI such as 'emboss needle'.


wsdl <- getURL("http://www.ebi.ac.uk/Tools/services/soap/emboss_needle?wsdl",  ssl.verifypeer = FALSE)
doc <- xmlInternalTreeParse(wsdl)
def <- processWSDL(doc)
ff <- genSOAPClientInterface(def = def)
#to get all parameters
ff at functions$getParameters()  ###it does really work 

but how to get the parameter details?

I try:

ff at functions$getParameterDetails(parameterId="asequence")

and error message as follow:
Error in as(list(parameterId = parameterId), "string") : 
  no method or default for coercing "list" to "string"

and i use the action of 'run' to do web service of 'emboss neddle' using:

###following were parameters:

email='luzifer.li at gmail.com'
myp at matrix='BLOSUM62'
myp at gapopen=10
myp at gapext=0.5
myp at endweight=FALSE
myp at endopen=10
myp at endextend=0.5
myp at format='pair'
myp at stype='protein'
myp at asequence<-"HEIAKGKAL"
myp at bsequence<-"HEIAKGKALIIIIEALKCLA"

####and use 'run' to do the web service:

ff at functions$run(email='luzifer.li at gmail.com',title='just_for_try',parameters=myp,.opts = list(ssl.verifypeer = FALSE))

and error message:

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "toSOAP", for signature "InputParameters", "XMLInternalElementNode", "missing"

Does anyone know why the above codes didn't work? 
Or anyone know someway to do web service of EMBL-EBI such as 'emboss needle'?



 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=Chinese_People's Republic of China.936  LC_CTYPE=Chinese_People's Republic of China.936    LC_MONETARY=Chinese_People's Republic of China.936
[4] LC_NUMERIC=C                                       LC_TIME=Chinese_People's Republic of China.936    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] XMLSchema_0.8-0    XML_3.9-4.1        SSOAP_0.91-0       RCurl_1.91-1.1     bitops_1.0-4.1     Biostrings_2.24.1  IRanges_1.14.4     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] codetools_0.2-8 stats4_2.15.1   tools_2.15.1  

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