Mercurial > repos > prog > lcmsmatching
diff UniProtCompound.R @ 0:e66bb061af06 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty
| author | prog |
|---|---|
| date | Tue, 12 Jul 2016 12:02:37 -0400 |
| parents | |
| children | 253d531a0193 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/UniProtCompound.R Tue Jul 12 12:02:37 2016 -0400 @@ -0,0 +1,81 @@ +if ( ! exists('UniprotCompound')) { # Do not load again if already loaded + + source('BiodbEntry.R') + + ##################### + # CLASS DECLARATION # + ##################### + + UniprotCompound <- setRefClass("UniprotCompound", contains = "BiodbEntry") + + ########### + # FACTORY # + ########### + + createUniprotCompoundFromXml <- function(contents, drop = FALSE) { + + library(XML) + + # Set XML namespace + ns <- c(uniprot = "http://uniprot.org/uniprot") + + compounds <- list() + + # Define xpath expressions + xpath.values <- character() + xpath.values[[RBIODB.NAME]] <- "/uniprot:uniprot/uniprot:compound/uniprot:name" + xpath.values[[RBIODB.GENE.SYMBOLS]] <- "//uniprot:gene/uniprot:name" + xpath.values[[RBIODB.FULLNAMES]] <- "//uniprot:protein//uniprot:fullName" + xpath.values[[RBIODB.SEQUENCE]] <- "//uniprot:entry/uniprot:sequence" + xpath.values[[RBIODB.ACCESSION]] <- "//uniprot:accession[1]" + xpath.attr <- list() + xpath.attr[[RBIODB.KEGG.ID]] <- list(path = "//uniprot:dbReference[@type='KEGG']", attr = 'id') + xpath.attr[[RBIODB.NCBI.GENE.ID]] <- list(path = "//uniprot:dbReference[@type='GeneID']", attr = 'id') + xpath.attr[[RBIODB.ENZYME.ID]] <- list(path = "//uniprot:dbReference[@type='EC']", attr = 'id') + xpath.attr[[RBIODB.MASS]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'mass') + xpath.attr[[RBIODB.LENGTH]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'length') + + for (content in contents) { + + # Create instance + compound <- HmdbCompound$new() + + # If the entity doesn't exist (i.e.: no <id>.xml page), then it returns an HTML page + if ( ! grepl("^<!DOCTYPE html ", content, perl = TRUE)) { + + # Parse XML + xml <- xmlInternalTreeParse(content, asText = TRUE) + + # Test value xpath + for (field in names(xpath.values)) { + v <- xpathSApply(xml, xpath.values[[field]], xmlValue, namespaces = ns) + if (length(v) > 0) + compound$setField(field, v) + } + + # Test attribute xpath + for (field in names(xpath.attr)) { + v <- xpathSApply(xml, xpath.attr[[field]]$path, xmlGetAttr, xpath.attr[[field]]$attr, namespaces = ns) + if (length(v) > 0) + compound$setField(field, v) + } + + # Remove new lines from sequence string + seq <- compound$getField(RBIODB.SEQUENCE) + if ( ! is.na(seq)) + compound$setField(RBIODB.SEQUENCE, gsub("\\n", "", seq)) + } + + compounds <- c(compounds, compound) + } + + # Replace elements with no accession id by NULL + compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x) + + # If the input was a single element, then output a single object + if (drop && length(contents) == 1) + compounds <- compounds[[1]] + + return(compounds) + } +}