Mercurial > repos > prog > lcmsmatching

annotate MassbankSpectrum.R @ 0:3afe41d3e9e7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
author prog
date Mon, 11 Jul 2016 09:12:03 -0400
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('MassbankSpectrum')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 source('BiodbEntry.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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4 source('MassbankCompound.R')
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6 ###########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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7 # MASSBANK SPECTRUM CLASS #
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8 ###########################
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9
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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10 MassbankSpectrum <- setRefClass("MassbankSpectrum", contains = "BiodbEntry")
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11
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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12 ###########
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13 # FACTORY #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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14 ###########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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16 createMassbankSpectrumFromTxt <- function(contents, drop = TRUE) {
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18 library(stringr)
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20 spectra <- list()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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22 # Define fields regex
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23 regex <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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24 regex[[RBIODB.ACCESSION]] <- "^ACCESSION: (.+)$"
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25 regex[[RBIODB.MSDEV]] <- "^AC\\$INSTRUMENT: (.+)$"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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26 regex[[RBIODB.MSDEVTYPE]] <- "^AC\\$INSTRUMENT_TYPE: (.+)$"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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27 regex[[RBIODB.MSTYPE]] <- "^AC\\$MASS_SPECTROMETRY: MS_TYPE (.+)$"
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28 regex[[RBIODB.MSPRECMZ]] <- "^MS\\$FOCUSED_ION: PRECURSOR_M/Z (.+)$"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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29 regex[[RBIODB.NB.PEAKS]] <- "^PK\\$NUM_PEAK: ([0-9]+)$"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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30 regex[[RBIODB.MSPRECANNOT]] <- "^MS\\$FOCUSED_ION: PRECURSOR_TYPE (.+)$"
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31
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32 for (text in contents) {
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33
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34 # Create instance
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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35 spectrum <- MassbankSpectrum$new()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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36
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37 # Read text
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38 lines <- strsplit(text, "\n")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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39 for (s in lines[[1]]) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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40
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41 # Test generic regex
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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42 parsed <- FALSE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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43 for (field in names(regex)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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44 g <- str_match(s, regex[[field]])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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45 if ( ! is.na(g[1,1])) {
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46 spectrum$setField(field, g[1,2])
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47 parsed <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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48 break
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49 }
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50 }
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51 if (parsed)
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52 next
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53
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54 # MS MODE
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55 g <- str_match(s, "^AC\\$MASS_SPECTROMETRY: ION_MODE (.+)$")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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56 if ( ! is.na(g[1,1])) {
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57 spectrum$setField(RBIODB.MSMODE, if (g[1,2] == 'POSITIVE') RBIODB.MSMODE.POS else RBIODB.MSMODE.NEG)
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58 next
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59 }
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60
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61 # PEAKS
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62 if (.parse.peak.line(spectrum, s))
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63 next
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64 }
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65
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66 spectra <- c(spectra, spectrum)
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67 }
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68
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69 # Replace elements with no accession id by NULL
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70 spectra <- lapply(spectra, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
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71
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72 # Set associated compounds
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73 compounds <- createMassbankCompoundFromTxt(contents)
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74 for (i in seq(spectra))
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75 if ( ! is.null(spectra[[i]]))
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76 spectra[[i]]$setField(RBIODB.COMPOUND, compounds[[i]])
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77
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78 # If the input was a single element, then output a single object
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79 if (drop && length(contents) == 1)
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80 spectra <- spectra[[1]]
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81
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82 return(spectra)
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83 }
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84
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85 ###################
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86 # PARSE PEAK LINE #
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87 ###################
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88
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89 .parse.peak.line <- function(spectrum, line) {
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90
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91 peaks <- RBIODB.PEAK.DF.EXAMPLE
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92
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93 # Annotation
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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94 g <- str_match(line, "^\\s+([0-9][0-9.]*) ([A-Z0-9+-]+) ([0-9]+) ([0-9][0-9.]*) ([0-9][0-9.]*)$")
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95 if ( ! is.na(g[1,1]))
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96 peaks[1, c(RBIODB.PEAK.MZ, RBIODB.PEAK.FORMULA, RBIODB.PEAK.FORMULA.COUNT, RBIODB.PEAK.MASS, RBIODB.PEAK.ERROR.PPM)] <- list(as.double(g[1,2]), g[1,3], as.integer(g[1,4]), as.double(g[1,5]), as.double(g[1,6]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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97
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98 # Peak
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99 g <- str_match(line, "^\\s+([0-9][0-9.]*) ([0-9][0-9.]*) ([0-9]+)$")
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100 if ( ! is.na(g[1,1]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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101 peaks[1, c(RBIODB.PEAK.MZ, RBIODB.PEAK.INTENSITY, RBIODB.PEAK.RELATIVE.INTENSITY)] <- list(as.double(g[1,2]), as.double(g[1,3]), as.integer(g[1,4]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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102
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103 if (nrow(peaks) > 0) {
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104
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105 # Get curent peaks and merge with new peaks
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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106 current.peaks <- spectrum$getField(RBIODB.PEAKS)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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107 if ( ! is.null(current.peaks))
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108 peaks <- rbind(current.peaks, peaks)
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109
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110 spectrum$setField(RBIODB.PEAKS, peaks)
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111
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112 return(TRUE)
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113 }
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114
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115 return(FALSE)
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116 }
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117 }