Mercurial > repos > prog > lcmsmatching
diff UniprotEntry.R @ 2:20d69a062da3 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
| author | prog |
|---|---|
| date | Thu, 02 Mar 2017 08:55:00 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/UniprotEntry.R Thu Mar 02 08:55:00 2017 -0500 @@ -0,0 +1,74 @@ +##################### +# CLASS DECLARATION # +##################### + +UniprotEntry <- methods::setRefClass("UniprotEntry", contains = "BiodbEntry") + +########### +# FACTORY # +########### + +createUniprotEntryFromXml <- function(contents, drop = FALSE) { + + # Set XML namespace + ns <- c(uniprot = "http://uniprot.org/uniprot") + + entries <- list() + + # Define xpath expressions + xpath.values <- character() + xpath.values[[BIODB.NAME]] <- "/uniprot:uniprot/uniprot:entry/uniprot:name" + xpath.values[[BIODB.GENE.SYMBOLS]] <- "//uniprot:gene/uniprot:name" + xpath.values[[BIODB.FULLNAMES]] <- "//uniprot:protein//uniprot:fullName" + xpath.values[[BIODB.SEQUENCE]] <- "//uniprot:entry/uniprot:sequence" + xpath.values[[BIODB.ACCESSION]] <- "//uniprot:accession[1]" + xpath.attr <- list() + xpath.attr[[BIODB.KEGG.ID]] <- list(path = "//uniprot:dbReference[@type='KEGG']", attr = 'id') + xpath.attr[[BIODB.NCBI.GENE.ID]] <- list(path = "//uniprot:dbReference[@type='GeneID']", attr = 'id') + xpath.attr[[BIODB.ENZYME.ID]] <- list(path = "//uniprot:dbReference[@type='EC']", attr = 'id') + xpath.attr[[BIODB.MASS]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'mass') + xpath.attr[[BIODB.LENGTH]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'length') + + for (content in contents) { + + # Create instance + entry <- UniprotEntry$new() + + # If the entity doesn't exist (i.e.: no <id>.xml page), then it returns an HTML page + if ( ! grepl("^<!DOCTYPE html ", content, perl = TRUE)) { + + # Parse XML + xml <- XML::xmlInternalTreeParse(content, asText = TRUE) + + # Test value xpath + for (field in names(xpath.values)) { + v <- XML::xpathSApply(xml, xpath.values[[field]], XML::xmlValue, namespaces = ns) + if (length(v) > 0) + entry$setField(field, v) + } + + # Test attribute xpath + for (field in names(xpath.attr)) { + v <- XML::xpathSApply(xml, xpath.attr[[field]]$path, XML::xmlGetAttr, xpath.attr[[field]]$attr, namespaces = ns) + if (length(v) > 0) + entry$setField(field, v) + } + + # Remove new lines from sequence string + seq <- entry$getField(BIODB.SEQUENCE) + if ( ! is.na(seq)) + entry$setField(BIODB.SEQUENCE, gsub("\\n", "", seq)) + } + + entries <- c(entries, entry) + } + + # Replace elements with no accession id by NULL + entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x) + + # If the input was a single element, then output a single object + if (drop && length(contents) == 1) + entries <- entries[[1]] + + return(entries) +}