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networkComplexityBigg/organismInformation/taxInfo.R

+#!/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)
+)
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