diff KeggCompound.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

--- a/KeggCompound.R	Tue Jul 12 12:02:37 2016 -0400
+++ b/KeggCompound.R	Sat Sep 03 17:02:01 2016 -0400
@@ -20,9 +20,9 @@
 	
 		# 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+)"
+		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) {
 
@@ -50,26 +50,26 @@
 					# ENZYME ID
 					g <- str_match(s, "^ENTRY\\s+EC\\s+(\\S+)")
 					if ( ! is.na(g[1,1]))
-						compound$setField(RBIODB.ACCESSION, paste('ec', g[1,2], sep = ':'))
+						compound$setField(BIODB.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$setField(RBIODB.ACCESSION, paste('cpd', g[1,2], sep = ':'))
+							compound$setField(BIODB.ACCESSION, paste('cpd', g[1,2], sep = ':'))
 
 						# OTHER ID
 						else {
 							g <- str_match(s, "^ENTRY\\s+(\\S+)")
 							if ( ! is.na(g[1,1]))
-								compound$setField(RBIODB.ACCESSION, g[1,2])
+								compound$setField(BIODB.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 = ':'))
+						compound$setField(BIODB.ACCESSION, paste(g[1,2], compound$getField(BIODB.ACCESSION), sep = ':'))
 				}
 			}
 
@@ -77,7 +77,7 @@
 		}
 
 		# Replace elements with no accession id by NULL
-		compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
+		compounds <- lapply(compounds, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
 
 		# If the input was a single element, then output a single object
 		if (drop && length(contents) == 1)