annotate KeggEntry.R @ 2:20d69a062da3 draft

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

#####################
# 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)
}