Mercurial > repos > prog > lcmsmatching
view EnzymeCompound.R @ 1:253d531a0193 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
author | prog |
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date | Sat, 03 Sep 2016 17:02:01 -0400 |
parents | e66bb061af06 |
children |
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if ( ! exists('EnzymeCompound')) { # Do not load again if already loaded source('BiodbEntry.R') ##################### # CLASS DECLARATION # ##################### EnzymeCompound <- setRefClass("EnzymeCompound", contains = 'BiodbEntry') ########### # FACTORY # ########### createEnzymeCompoundFromTxt <- function(contents, drop = TRUE) { library(stringr) compounds <- list() # Define fields regex regex <- character() regex[[BIODB.ACCESSION]] <- "^ID\\s+([0-9.]+)$" regex[[BIODB.DESCRIPTION]] <- "^DE\\s+(.+)$" for (text in contents) { # Create instance compound <- EnzymeCompound$new() lines <- strsplit(text, "\n") for (s in lines[[1]]) { # Test generic regex parsed <- FALSE for (field in names(regex)) { g <- str_match(s, regex[[field]]) if ( ! is.na(g[1,1])) { compound$setField(field, g[1,2]) parsed <- TRUE break } } if (parsed) next } 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]] return(compounds) } }