Mercurial > repos > tomnl > cameradims
annotate cameradims.R @ 19:d4081e4160af draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author | tomnl |
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date | Thu, 21 Jun 2018 08:47:44 -0400 |
parents | fe9a6e7bbebb |
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rev | line source |
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55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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1 library(optparse) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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2 library(cameraDIMS) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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3 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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4 option_list <- list( |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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5 make_option(c("-i", "--in_file"), type="character"), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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6 make_option(c("-o", "--out_dir"), type="character"), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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7 make_option("--ppm_iso", default=5), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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8 make_option("--ppm_adduct", default=5), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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9 make_option("--maxiso", default=4), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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10 make_option("--mzabs_iso", default=0.015), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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11 make_option("--mzabs_adduct", default=0.015), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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12 make_option("--maxcharge", default=3), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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13 make_option("--maxmol", default=3), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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14 make_option("--polarity", default='pos'), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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15 make_option("--rule_path"), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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16 make_option("--rule_type"), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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17 make_option("--export_ruleset", action="store_true"), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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18 make_option("--intensity_filter", default=0) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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19 ) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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20 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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21 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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22 # store options |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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23 opt<- parse_args(OptionParser(option_list=option_list)) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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24 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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25 print(sessionInfo()) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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26 print(opt) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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27 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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28 df <- read.table(opt$in_file, header = TRUE, sep='\t', stringsAsFactors=FALSE) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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29 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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30 print('IN DATA') |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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31 print(nrow(df)) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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32 print(head(df)) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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33 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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34 devppm_adduct <- opt$ppm_adduct / 1000000 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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35 devppm_iso <- opt$ppm_iso / 1000000 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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36 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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37 paramiso <- list("ppm"=opt$ppm_iso, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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38 "filter"=TRUE, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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39 "maxcharge"=opt$maxcharge, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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40 "maxiso"=opt$maxiso, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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41 "mzabs"=opt$mzabs_iso, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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42 "intval"='maxo', |
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d4081e4160af
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
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43 "minfrac"=1, |
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55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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44 'IM'=NULL, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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45 'devppm'=devppm_iso) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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46 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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47 paramadduct <- list("maxCharge"= opt$maxcharge, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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48 "maxMol"= opt$maxmol, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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49 'devppm'=devppm_adduct, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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50 "mzabs"=opt$mzabs_adduct, |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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51 'IM'=NULL, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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52 "filter"=TRUE, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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53 'ppm'=opt$ppm_adduct, |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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54 "quasimolion"= c(1, 6, 8), |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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55 'polarity'=opt$polarity) |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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56 |
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57 |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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58 |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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59 |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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60 if(is.null(opt$export_ruleset)){ |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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61 rule_export <- FALSE |
55aa2dd24828
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62 }else{ |
55aa2dd24828
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63 rule_export <- TRUE |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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64 } |
55aa2dd24828
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65 |
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66 df$mz <- as.numeric(df$mz) |
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67 |
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68 print(head(df$mz)) |
55aa2dd24828
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69 |
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70 if ('intensity' %in% colnames(df)){ |
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71 colnames(df)[colnames(df)=='intensity'] = 'i' |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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72 } |
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73 |
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74 if (!'peakID' %in% colnames(df)){ |
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75 df <- cbind('peakID'=1:nrow(df), df) |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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76 } |
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77 |
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78 df$i <- as.numeric(df$i) |
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79 |
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80 df <- df[df$i>opt$intensity_filter,] |
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81 |
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82 if (nrow(df)==0){ |
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83 print('No peaks left after filtering') |
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84 quit() |
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85 } |
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86 |
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87 |
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88 if (opt$rule_type=='extended_large'){ |
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89 |
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90 rule_sep=',' |
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91 opt$rule_type <- 'user' |
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92 if(opt$polarity=='pos'){ |
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93 opt$rule_path <- system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS") |
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94 }else{ |
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95 opt$rule_path <- system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS") |
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96 } |
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97 }else{ |
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98 rule_sep='\t' |
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99 } |
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100 |
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101 cameraOut <- cameraDIMS(data=df, |
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102 params_iso=paramiso, |
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103 params_adduct=paramadduct, |
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104 rule_type=opt$rule_type, |
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105 rule_pth=opt$rule_path, |
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106 rule_sep=rule_sep, |
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107 rule_export=rule_export) |
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108 |
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109 |
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110 print(head(cameraOut[[1]])) |
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111 print(head(cameraOut[[2]])) |
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112 |
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113 |
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114 out_file1 <- file.path(opt$out_dir, 'camera_annotated_peaklist.txt') |
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115 out_file2 <- file.path(opt$out_dir, 'camera_annotated_map.txt') |
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116 out_file3 <- file.path(opt$out_dir, 'ruleset.txt') |
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117 |
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118 write.table(cameraOut[[1]], out_file1, row.names=FALSE, sep='\t') |
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119 write.table(cameraOut[[2]], out_file2, row.names=FALSE, sep='\t') |
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120 |
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121 if (rule_export){ |
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122 write.table(cameraOut[[3]], out_file3, row.names=FALSE, sep='\t') |
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123 } |