Hi everybody,

I have some difficulties to use regular expressions in R. 
My problem is that I can't recover in a vector the data that I want to recover. 

My R script is the next:

variable<-file("BestFitnessSBML_L1V2_exported.xml", open="r")
while (length(line <- readLines(variable, n = 1))) {
  results<-grep('.*<parameter name=\"a1\" value=\"0.1\"/>.*', line, perl = TRUE, ignore.case = TRUE) 
  print(results)
}
close(fichier)

When I print results I see that the regular expression has been found in my file.

I want to recover a1 and 0.1 in the regular expressions '.*<parameter name=\"a1\" value=\"0.1\"/>.*'. Maybe someone can explain me how to recover it ?
 

Cordially,

Fabien

Diego is right to suggest that using regular expressions is not the right way to go. Instead read the file using the XML package

library(XML)
xml = xmlParse("BestFitnessSBML_L1V2_exported.xml")

 and then query it using an 'xpath', with the Abbreviate Syntax of the specification a surprisingly helpful place to start. You might be able to extract the name / value pairs as

name = sapply(xml["//parameter", xmlAttrs, "name")
value = as.numeric(sapply(xml["//parameter", xmlAttrs, "value"))

There are SBML parsing facilities in Bioconductor (rsbml, SBMLR) but I'm not familiar enough with these to know whether they are helpful in this case.

You are trying to parse XML with regular expressions but maybe you should use the XML package instead? This reminds me of this (famous) question and answer (the top one) in SO (which you may be interested in checking): http://stackoverflow.com/questions/1732348/regex-match-open-tags-except-xhtml-self-contained-tags