comparison NcbiGeneCompound.R @ 1:253d531a0193 draft

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

0:e66bb061af06

		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()

				}
			
				# 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]]
	

1:253d531a0193

		compounds <- list()

		# Define xpath expressions
		xpath.expr <- character()
		xpath.expr[[BIODB.ACCESSION]] <- "//Gene-track_geneid"
		xpath.expr[[BIODB.KEGG.ID]] <- "/Dbtag_db[text()='KEGG']/..//Object-id_str"
		xpath.expr[[BIODB.UNIPROT.ID]] <- "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str"
		xpath.expr[[BIODB.LOCATION]] <- "//Gene-ref_maploc"
		xpath.expr[[BIODB.PROTEIN.DESCRIPTION]] <- "//Gene-ref_desc"
		xpath.expr[[BIODB.SYMBOL]] <- "//Gene-ref_locus"
		xpath.expr[[BIODB.SYNONYMS]] <- "//Gene-ref_syn_E"

		for (content in contents) {

			# Create instance
			compound <- NcbigeneCompound$new()

				}
			
				# CCDS ID
				ccdsid <- .find.ccds.id(xml)
				if ( ! is.na(ccdsid))
					compound$setField(BIODB.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(BIODB.ACCESSION))) NULL else x)

		# If the input was a single element, then output a single object
		if (drop && length(contents) == 1)
			compounds <- compounds[[1]]