Mercurial > repos > prog > lcmsmatching

annotate LipidmapsEntry.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 LipidmapsEntry <- methods::setRefClass("LipidmapsEntry", contains = 'BiodbEntry')
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7 ###########
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8 # FACTORY #
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9 ###########
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11 createLipidmapsEntryFromCsv <- function(contents, drop = TRUE) {
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13 entries <- list()
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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15 # Mapping column names
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16 col2field <- list()
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17 col2field[[BIODB.NAME]] <- 'COMMON_NAME'
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18 col2field[[BIODB.ACCESSION]] <- 'LM_ID'
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19 col2field[[BIODB.KEGG.ID]] <- 'KEGG_ID'
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20 col2field[[BIODB.HMDB.ID]] <- 'HMDBID'
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21 col2field[[BIODB.MASS]] <- 'MASS'
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22 col2field[[BIODB.FORMULA]] <- 'FORMULA'
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24 for (text in contents) {
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26 # Create instance
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27 entry <- LipidmapsEntry$new()
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29 # Split text in lines
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30 lines <- split.str(text, sep = "\n", unlist = TRUE)
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32 # An error occured
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33 if ( ! grepl("No record found", lines[[2]])) {
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35 # Keys on first line
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36 keys <- split.str(lines[[1]], unlist = TRUE)
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38 # Values on second line
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39 values <- split.str(lines[[2]], unlist = TRUE)
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40 names(values) <- keys[seq(values)]
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42 # Get field values
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43 for (field in names(col2field))
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44 if (values[[col2field[[field]]]] != '-')
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45 entry$setField(field, values[[col2field[[field]]]])
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47 # Set names
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48 if (values[['SYNONYMS']] != '-') {
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49 # TODO
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50 }
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51 }
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52
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53 entries <- c(entries, entry)
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54 }
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55
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56 # Replace elements with no accession id by NULL
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57 entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
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58
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59 # If the input was a single element, then output a single object
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60 if (drop && length(contents) == 1)
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61 entries <- entries[[1]]
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62
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63 return(entries)
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64 }