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annotate combineAnnotations.R @ 3:7c0834ead235 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
author tomnl
date Tue, 18 Jun 2019 10:04:42 -0400
parents f075f67c7416
children 7a3f8bd7757d
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1 library(optparse)
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2 library(msPurity)
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3 print(sessionInfo())
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5 # Get the parameter
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6 option_list <- list(
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7 make_option(c("-s","--sm_resultPth"),type="character"),
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8 make_option(c("-m","--metfrag_resultPth"),type="character"),
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9 make_option(c("-c","--sirius_csi_resultPth"),type="character"),
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10 make_option(c("-p","--probmetab_resultPth"),type="character"),
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11 make_option(c("-sw","--sm_weight"),type="numeric"),
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12 make_option(c("-mw","--metfrag_weight"),type="numeric"),
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13 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
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14 make_option(c("-pw","--probmetab_weight"),type="numeric"),
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15 make_option("--create_new_database", action="store_true"),
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16 make_option(c("-o","--outdir"),type="character", default="."),
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17 make_option("--eic", action="store_true")
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18 )
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19 opt <- parse_args(OptionParser(option_list=option_list))
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21 print(opt)
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23 if (!is.null(opt$create_new_database)){
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24 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
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25 file.copy(opt$sm_resultPth, sm_resultPth)
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26 }else{
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27 sm_resultPth <- opt$sm_resultPth
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28 }
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31 weights <-list('sm'=opt$sm_weight,
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32 'metfrag'=opt$metfrag_weight,
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33 'sirius_csifingerid'= opt$sirius_csi_weight,
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34 'probmetab'=opt$probmetab_weight
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35 )
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37 if (round(!sum(unlist(weights),0)==1)){
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39 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
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40 }
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42 summary_output <- msPurity::combineAnnotations(sm_resultPth,
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43 opt$metfrag_resultPth,
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44 opt$sirius_csi_resultPth,
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45 opt$probmetab_resultPth,
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46 weights = weights)
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48 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
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50 if (!is.null(opt$eic)){
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52 if (is.null(xset)){
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53 xset <- xa@xcmsSet
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54 }
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55 # previous check should have matched filelists together
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56 xset@filepaths <- unname(pa@fileList)
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58 convert2Raw <- function(x, xset){
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59 sid <- unique(x$sample)
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60 # for each file get list of peaks
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61 x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
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62 x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
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63 x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
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64 return(x)
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66 }
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68 xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
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70 # Saves the EICS into the previously created database
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71 px <- msPurity::purityX(xset, saveEIC = TRUE,
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72 cores=1, sqlitePth=db_pth,
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73 rtrawColumns = TRUE)
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75 }
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77 closeAllConnections()
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