diff KeggCompound.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/KeggCompound.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,88 @@
+if ( ! exists('KeggCompound')) { # Do not load again if already loaded
+
+	source('BiodbEntry.R')
+	
+	#####################
+	# CLASS DECLARATION #
+	#####################
+	
+	KeggCompound <- setRefClass("KeggCompound", contains = 'BiodbEntry')
+	
+	###########
+	# FACTORY #
+	###########
+	
+	createKeggCompoundFromTxt <- function(contents, drop = TRUE) {
+	
+		library(stringr)
+
+		compounds <- list()
+	
+		# Define fields regex
+		regex <- character()
+		regex[[RBIODB.NAME]] <- "^NAME\\s+([^,;]+)"
+		regex[[RBIODB.CHEBI.ID]] <- "^\\s+ChEBI:\\s+(\\S+)"
+		regex[[RBIODB.LIPIDMAPS.ID]] <- "^\\s+LIPIDMAPS:\\s+(\\S+)"
+
+		for (text in contents) {
+
+			# Create instance
+			compound <- KeggCompound$new()
+
+			lines <- strsplit(text, "\n")
+			for (s in lines[[1]]) {
+
+				# Test generic regex
+				parsed <- FALSE
+				for (field in names(regex)) {
+					g <- str_match(s, regex[[field]])
+					if ( ! is.na(g[1,1])) {
+						compound$setField(field, g[1,2])
+						parsed <- TRUE
+						break
+					}
+				}
+				if (parsed)
+					next
+	
+				# ACCESSION
+				{
+					# ENZYME ID
+					g <- str_match(s, "^ENTRY\\s+EC\\s+(\\S+)")
+					if ( ! is.na(g[1,1]))
+						compound$setField(RBIODB.ACCESSION, paste('ec', g[1,2], sep = ':'))
+
+					# ENTRY ID
+					else {
+						g <- str_match(s, "^ENTRY\\s+(\\S+)\\s+Compound")
+						if ( ! is.na(g[1,1]))
+							compound$setField(RBIODB.ACCESSION, paste('cpd', g[1,2], sep = ':'))
+
+						# OTHER ID
+						else {
+							g <- str_match(s, "^ENTRY\\s+(\\S+)")
+							if ( ! is.na(g[1,1]))
+								compound$setField(RBIODB.ACCESSION, g[1,2])
+						}
+					}
+	
+					# ORGANISM
+					g <- str_match(s, "^ORGANISM\\s+(\\S+)")
+					if ( ! is.na(g[1,1]))
+						compound$setField(RBIODB.ACCESSION, paste(g[1,2], compound$getField(RBIODB.ACCESSION), sep = ':'))
+				}
+			}
+
+			compounds <- c(compounds, compound)
+		}
+
+		# Replace elements with no accession id by NULL
+		compounds <- lapply(compounds, function(x) if (is.na(x$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)
+	}
+}