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annotate msdb-common.R @ 6:b8f70d8216b3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
author prog
date Mon, 27 Mar 2017 06:27:29 -0400
parents 1ba222315fd5
children
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('.parse_chrom_col_desc')) { # 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 library('stringr')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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4 source('strhlp.R', chdir = TRUE)
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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5 source('biodb-common.R', chdir = TRUE)
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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7 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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8 # CONSTANTS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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9 #############
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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11 # Field tags
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12 MSDB.TAG.MZ <- 'mz'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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13 MSDB.TAG.MZEXP <- 'mzexp'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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14 MSDB.TAG.MZTHEO <- 'mztheo'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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15 MSDB.TAG.RT <- 'rt'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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16 MSDB.TAG.MODE <- 'msmode'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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17 MSDB.TAG.MOLID <- 'compoundid'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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18 MSDB.TAG.COL <- 'chromcol'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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19 MSDB.TAG.COLRT <- 'chromcolrt'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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20 MSDB.TAG.ATTR <- 'peakattr'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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21 MSDB.TAG.INT <- 'intensity'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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22 MSDB.TAG.REL <- 'relative.intensity'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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23 MSDB.TAG.COMP <- 'peakcomp'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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24 MSDB.TAG.MOLNAMES <- 'fullnames'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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25 MSDB.TAG.MOLCOMP <- 'compoundmass'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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26 MSDB.TAG.MOLMASS <- 'compoundcomp'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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27 MSDB.TAG.INCHI <- 'inchi'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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28 MSDB.TAG.INCHIKEY <- 'inchikey'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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29 MSDB.TAG.PUBCHEM <- 'pubchemcompid'
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30 MSDB.TAG.CHEBI <- 'chebiid'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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31 MSDB.TAG.HMDB <- 'hmdbid'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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32 MSDB.TAG.KEGG <- 'keggid'
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34 # Mode tags
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35 MSDB.TAG.POS <- 'neg'
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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36 MSDB.TAG.NEG <- 'pos'
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38 # Fields containing multiple values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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39 MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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40 MSDB.MULTIVAL.FIELD.SEP <- ';'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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42 # Authorized mz tolerance unit values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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43 MSDB.MZTOLUNIT.PPM <- 'ppm'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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44 MSDB.MZTOLUNIT.PLAIN <- 'plain' # same as mz: mass-to-charge ratio
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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45 MSDB.MZTOLUNIT.VALS <- c(MSDB.MZTOLUNIT.PPM, MSDB.MZTOLUNIT.PLAIN)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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46
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47 # Authorized rt units
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48 MSDB.RTUNIT.SEC <- 'sec'
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49 MSDB.RTUNIT.MIN <- 'min'
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50 MSDB.RTUNIT.VALS <- c(MSDB.RTUNIT.SEC ,MSDB.RTUNIT.MIN)
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51
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52 # Default values
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53 MSDB.DFT.PREC <- list()
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54 MSDB.DFT.PREC[[MSDB.TAG.POS]] <- c("[(M+H)]+", "[M+H]+", "[(M+Na)]+", "[M+Na]+", "[(M+K)]+", "[M+K]+")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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55 MSDB.DFT.PREC[[MSDB.TAG.NEG]] <- c("[(M-H)]-", "[M-H]-", "[(M+Cl)]-", "[M+Cl]-")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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56 MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP <- MSDB.MULTIVAL.FIELD.SEP
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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57 MSDB.DFT.MATCH.FIELDS <- list( molids = 'molid', molnames = 'molnames')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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58 MSDB.DFT.MATCH.SEP <- ','
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59 MSDB.DFT.MODES <- list( pos = 'POS', neg = 'NEG')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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60 MSDB.DFT.MZTOLUNIT <- MSDB.MZTOLUNIT.PPM
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61
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62 ############################
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63 # GET DEFAULT INPUT FIELDS #
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64 ############################
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66 msdb.get.dft.input.fields <- function () {
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68 dft.fields <- list()
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70 for(f in c(MSDB.TAG.MZ, MSDB.TAG.RT))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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71 dft.fields[[f]] <- f
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73 return(dft.fields)
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74 }
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76 #########################
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77 # GET DEFAULT DB FIELDS #
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78 #########################
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80 msdb.get.dft.db.fields <- function () {
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81
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82 dft.fields <- list()
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84 for (f in c(MSDB.TAG.MZTHEO, MSDB.TAG.COLRT, MSDB.TAG.MOLID, MSDB.TAG.COL, MSDB.TAG.MODE, MSDB.TAG.ATTR, MSDB.TAG.COMP, MSDB.TAG.MOLNAMES, MSDB.TAG.MOLCOMP, MSDB.TAG.MOLMASS, MSDB.TAG.INCHI, MSDB.TAG.INCHIKEY, MSDB.TAG.PUBCHEM, MSDB.TAG.CHEBI, MSDB.TAG.HMDB, MSDB.TAG.KEGG))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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85 dft.fields[[f]] <- f
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86
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87 return(dft.fields)
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88 }
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90 ##################
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91 # MAKE DB FIELDS #
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92 ##################
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93
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94 msdb.make.db.fields <- function(fields) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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95
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96 # Merge with default fields
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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97 dft.fields <- msdb.get.dft.db.fields()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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98 absent <- ! names(dft.fields) %in% names(fields)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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99 if (length(absent) > 0)
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100 fields <- c(fields, dft.fields[absent])
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101
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102 return(fields)
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103 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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104
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105 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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106 # MAKE INPUT DATA FRAME #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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107 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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108
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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109 msdb.make.input.df <- function(mz, rt = NULL, rtunit = MSDB.RTUNIT.SEC) {
0
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110
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111 field <- msdb.get.dft.input.fields()
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112
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113 x <- data.frame()
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114
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115 # Set mz
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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116 if (length(mz) > 1)
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117 x[seq(mz), field[[MSDB.TAG.MZ]]] <- mz
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118 else if (length(mz) == 1)
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119 x[1, field[[MSDB.TAG.MZ]]] <- mz
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120 else
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121 x[, field[[MSDB.TAG.MZ]]] <- numeric()
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122
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123 # Set rt
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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124 if ( ! is.null(rt)) {
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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125 if (rtunit == MSDB.RTUNIT.MIN)
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126 rtunit <- rtunit * 60
0
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127 if (length(rt) > 1)
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128 x[seq(rt), field[[MSDB.TAG.RT]]] <- rt
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129 else if (length(rt) == 1)
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130 x[1, field[[MSDB.TAG.RT]]] <- rt
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131 else
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132 x[, field[[MSDB.TAG.RT]]] <- numeric()
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133 }
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134
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135 return(x)
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136 }
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137
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138 ###############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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139 # GET EMPTY RESULT DATA FRAME #
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140 ###############################
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141
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142 .get.empty.result.df <- function(rt = FALSE) {
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143
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144 df <- data.frame(stringsAsFactors = FALSE)
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145 df[MSDB.TAG.MOLID] <- character()
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146 df[MSDB.TAG.MOLNAMES] <- character()
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147 df[MSDB.TAG.MZ] <- numeric()
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148 df[MSDB.TAG.MZTHEO] <- numeric()
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149 df[MSDB.TAG.ATTR] <- character()
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150 df[MSDB.TAG.COMP] <- character()
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151 if (rt) {
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152 df[MSDB.TAG.RT] <- numeric()
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153 df[MSDB.TAG.COL] <- character()
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154 df[MSDB.TAG.COLRT] <- numeric()
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155 }
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156
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157 return(df)
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158 }
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159
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160 ############################
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161 # PARSE COLUMN DESCRIPTION #
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162 ############################
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163
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164 .parse_chrom_col_desc <- function(desc) {
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165
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166 # Clean string
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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167 s <- desc
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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168 s <- gsub('\\.+', ' ', s, perl = TRUE) # Replace '.' characters by spaces
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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169 s <- gsub('[*-]', ' ', s, perl = TRUE) # Replace dashes and asterisks by spaces
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170 s <- gsub('[)(]', '', s, perl = TRUE) # Remove paranthesis
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171 s <- trim(s)
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172 s <- tolower(s) # put in lowercase
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173
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174 # Match 2 3 4 5 6 7 8 9 10 1112 13
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175 pattern <- "^(uplc|hsf5|hplc|zicphilic)( (c8|c18|150 5 2 1))?( (\\d+)mn)?( (orbitrap|exactive|qtof|shimadzu exactive))?( (\\d+)mn)?( (bis|ter))?( 1)?$"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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176 g <- str_match(s, pattern)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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177 if (is.na(g[1, 1]))
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178 stop(paste0("Impossible to parse column description \"", desc, "\"."))
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179
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180 type <- g[1, 2]
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181 stationary_phase <- if ( ! is.na(g[1, 4]) && nchar(g[1, 4]) > 0) g[1, 4] else NA_character_
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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182 msdevice <- if ( ! is.na(g[1, 8]) && nchar(g[1, 8]) > 0) g[1, 8] else NA_character_
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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183 time <- if ( ! is.na(g[1,6]) && nchar(g[1, 6]) > 0) as.integer(g[1, 6]) else ( if ( ! is.na(g[1, 10]) && nchar(g[1, 10]) > 0) as.integer(g[1, 10]) else NA_integer_ )
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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184
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185 # Correct values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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186 if ( ! is.na(stationary_phase) && stationary_phase == '150 5 2 1') stationary_phase <- '150*5*2.1'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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187 if ( ! is.na(msdevice)) msdevice <- gsub(' ', '', msdevice) # remove spaces
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188
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189 return(list( type = type, stationary_phase = stationary_phase, time = time, msdevice = msdevice))
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190
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191 }
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192
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193 #########################
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194 # NORMALIZE COLUMN NAME #
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195 #########################
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196
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197 .normalize_column_name <- function(desc) {
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198
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199 lst <- .parse_chrom_col_desc(desc)
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200
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201 v <- c(lst$type)
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202 if ( ! is.na(lst$stationary_phase))
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203 v <- c(v, lst$stationary_phase)
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204 if ( ! is.na(lst$time))
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205 v <- c(v, paste0(lst$time, "min"))
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206 if ( ! is.na(lst$msdevice))
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207 v <- c(v, lst$msdevice)
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208
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209 return(paste(v, collapse = '-'))
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210 }
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211
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212 } # end of load safe guard