diff KeggEntry.R @ 1:45e985cd8e9e draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/KeggEntry.R	Tue Jan 31 05:27:24 2017 -0500
@@ -0,0 +1,81 @@
+#####################
+# CLASS DECLARATION #
+#####################
+
+KeggEntry <- methods::setRefClass("KeggEntry", contains = 'BiodbEntry')
+
+###########
+# FACTORY #
+###########
+
+createKeggEntryFromTxt <- function(contents, drop = TRUE) {
+
+	entries <- list()
+
+	# Define fields regex
+	regex <- character()
+	regex[[BIODB.NAME]] <- "^NAME\\s+([^,;]+)"
+	regex[[BIODB.CHEBI.ID]] <- "^\\s+ChEBI:\\s+(\\S+)"
+	regex[[BIODB.LIPIDMAPS.ID]] <- "^\\s+LIPIDMAPS:\\s+(\\S+)"
+
+	for (text in contents) {
+
+		# Create instance
+		entry <- KeggEntry$new()
+
+		lines <- strsplit(text, "\n")
+		for (s in lines[[1]]) {
+
+			# Test generic regex
+			parsed <- FALSE
+			for (field in names(regex)) {
+				g <- stringr::str_match(s, regex[[field]])
+				if ( ! is.na(g[1,1])) {
+					entry$setField(field, g[1,2])
+					parsed <- TRUE
+					break
+				}
+			}
+			if (parsed)
+				next
+
+			# ACCESSION
+			{
+				# ENZYME ID
+				g <- stringr::str_match(s, "^ENTRY\\s+EC\\s+(\\S+)")
+				if ( ! is.na(g[1,1])){
+					entry$setField(BIODB.ACCESSION, paste('ec', g[1,2], sep = ':'))
+
+				# ENTRY ID
+				}else {
+					g <- stringr::str_match(s, "^ENTRY\\s+(\\S+)\\s+Compound")
+					if ( ! is.na(g[1,1])){
+						entry$setField(BIODB.ACCESSION, paste('cpd', g[1,2], sep = ':'))
+
+					# OTHER ID
+					}else {
+						g <- stringr::str_match(s, "^ENTRY\\s+(\\S+)")
+						if ( ! is.na(g[1,1]))
+							entry$setField(BIODB.ACCESSION, g[1,2])
+					}
+				}
+
+				# ORGANISM
+				g <- stringr::str_match(s, "^ORGANISM\\s+(\\S+)")
+				if ( ! is.na(g[1,1]))
+					entry$setField(BIODB.ACCESSION, paste(g[1,2], entry$getField(BIODB.ACCESSION), sep = ':'))
+			}
+		}
+
+		entries <- c(entries, entry)
+	}
+
+	# Replace elements with no accession id by NULL
+	entries <- lapply(entries, function(x) if (is.na(x$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)
+}