diff --git a/networkComplexityBigg/organismInformation/taxInfo.R b/networkComplexityBigg/organismInformation/taxInfo.R new file mode 100644 index 0000000000000000000000000000000000000000..891c42c08bad4ac269801a27e0341806340adcdc --- /dev/null +++ b/networkComplexityBigg/organismInformation/taxInfo.R @@ -0,0 +1,35 @@ +#!/usr/bin/Rscript +library(methods) +library(dplyr) +library(XML) + +modelTable <- read.csv("../envirDist/modelTable.csv") + + +xmlURL <- paste0("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&retmode=xml&id=", + paste(modelTable$taxid, collapse=",")) +xmlText <- paste(scan(xmlURL, what="",sep="\n"),"\n",collapse="\n") +doc <- xmlParse(xmlText) + + +getNodeSet(doc, "/TaxaSet/Taxon/Lineage") + + +modelTableTaxonInformation <- data.frame(bigg_id=modelTable$bigg_id, +taxid=xpathSApply(doc, "/TaxaSet/Taxon/TaxId", xmlValue), +name=xpathSApply(doc, "/TaxaSet/Taxon/ScientificName", xmlValue), +division=xpathSApply(doc, "/TaxaSet/Taxon/Division", xmlValue), +lineage=xpathSApply(doc, "/TaxaSet/Taxon/Lineage", xmlValue) +) + + + + + + + + + + + +