diff NcbiGeneCompound.R @ 0:e66bb061af06 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NcbiGeneCompound.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,118 @@
+if ( ! exists('NcbigeneCompound')) { # Do not load again if already loaded
+
+	source('BiodbEntry.R')
+	source(file.path('strhlp.R'), chdir = TRUE)
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+
+	NcbigeneCompound <- setRefClass("NcbigeneCompound", contains = "BiodbEntry")
+
+	###########
+	# FACTORY #
+	###########
+
+	createNcbigeneCompoundFromXml <- function(contents, drop = TRUE) {
+
+		library(XML)
+
+		compounds <- list()
+
+		# Define xpath expressions
+		xpath.expr <- character()
+		xpath.expr[[RBIODB.ACCESSION]] <- "//Gene-track_geneid"
+		xpath.expr[[RBIODB.KEGG.ID]] <- "/Dbtag_db[text()='KEGG']/..//Object-id_str"
+		xpath.expr[[RBIODB.UNIPROT.ID]] <- "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str"
+		xpath.expr[[RBIODB.LOCATION]] <- "//Gene-ref_maploc"
+		xpath.expr[[RBIODB.PROTEIN.DESCRIPTION]] <- "//Gene-ref_desc"
+		xpath.expr[[RBIODB.SYMBOL]] <- "//Gene-ref_locus"
+		xpath.expr[[RBIODB.SYNONYMS]] <- "//Gene-ref_syn_E"
+
+		for (content in contents) {
+
+			# Create instance
+			compound <- NcbigeneCompound$new()
+		
+			# Parse HTML
+			xml <-  xmlInternalTreeParse(content, asText = TRUE)
+
+			# An error occured
+			if (length(getNodeSet(xml, "//Error")) == 0 && length(getNodeSet(xml, "//ERROR")) == 0) {
+
+				# Test generic xpath expressions
+				for (field in names(xpath.expr)) {
+					v <- xpathSApply(xml, xpath.expr[[field]], xmlValue)
+					if (length(v) > 0) {
+
+						# Eliminate duplicates
+						v <- v[ ! duplicated(v)]
+
+						# Set field
+						compound$setField(field, v)
+					}
+				}
+			
+				# CCDS ID
+				ccdsid <- .find.ccds.id(xml)
+				if ( ! is.na(ccdsid))
+					compound$setField(RBIODB.NCBI.CCDS.ID, ccdsid)
+			}
+
+			compounds <- c(compounds, compound)
+		}
+
+		# Replace elements with no accession id by NULL
+		compounds <- lapply(compounds, function(x) if (is.na(x$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)
+
+		# Get data
+
+	}
+
+	################
+	# FIND CCDS ID #
+	################
+
+	.find.ccds.id <- function(xml) {
+
+		# 1) Get all CCDS tags.
+		ccds_elements <- getNodeSet(xml, "//Dbtag_db[text()='CCDS']/..//Object-id_str")
+
+		# 2) If all CCDS are the same, go to point 4.
+		ccds <- NA_character_
+		for (e in ccds_elements) {
+			current_ccds <- xmlValue(e)
+			if (is.na(ccds))
+				ccds <- current_ccds
+			else {
+				if (current_ccds != ccds) {
+					ccds <- NA_character_
+					break
+				}
+			}
+		}
+
+		# 3) There are several CCDS values, we need to find the best one (i.e.: the most current one).
+		if (is.na(ccds)) {
+			# For each CCDS, look for the parent Gene-commentary tag. Then look for the text content of the Gene-commentary_label which is situed under. Ignore CCDS that have no Gene-commentary_label associated. Choose the CCDS that has the smallest Gene-commentary_label in alphabetical order.
+			version <- NA_character_
+			for (e in ccds_elements) {
+				versions <- xpathSApply(e, "ancestor::Gene-commentary/Gene-commentary_label", xmlValue)
+				if (length(versions) < 1) next
+				current_version <- versions[[length(versions)]]
+				if (is.na(version) || current_version < version) {
+					version <- current_version
+					ccds <- xmlValue(e)
+				}
+			}
+		}
+
+		return(ccds)
+	}
+}