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annotate msdb-common.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents 3afe41d3e9e7
children 1ba222315fd5
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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
1
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12 MSDB.TAG.MZ <- BIODB.PEAK.MZ
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13 MSDB.TAG.MZEXP <- BIODB.PEAK.MZEXP
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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14 MSDB.TAG.MZTHEO <- BIODB.PEAK.MZTHEO
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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15 MSDB.TAG.RT <- BIODB.PEAK.RT
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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16 MSDB.TAG.MODE <- BIODB.MSMODE
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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17 MSDB.TAG.MOLID <- BIODB.COMPOUND.ID
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18 MSDB.TAG.COL <- BIODB.CHROM.COL
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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19 MSDB.TAG.COLRT <- BIODB.CHROM.COL.RT
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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20 MSDB.TAG.ATTR <- BIODB.PEAK.ATTR
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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21 MSDB.TAG.INT <- BIODB.PEAK.INTENSITY
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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22 MSDB.TAG.REL <- BIODB.PEAK.RELATIVE.INTENSITY
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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23 MSDB.TAG.COMP <- BIODB.PEAK.COMP
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24 MSDB.TAG.MOLNAMES <- BIODB.FULLNAMES
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25 MSDB.TAG.MOLCOMP <- BIODB.COMPOUND.MASS
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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26 # MSDB.TAG.MOLATTR <- 'molattr'
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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27 MSDB.TAG.MOLMASS <- BIODB.COMPOUND.COMP
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28 MSDB.TAG.INCHI <- BIODB.INCHI
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29 MSDB.TAG.INCHIKEY <- BIODB.INCHIKEY
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30 # TODO Use BIODB tags.
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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31 MSDB.TAG.PUBCHEM <- BIODB.PUBCHEMCOMP.ID
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32 MSDB.TAG.CHEBI <- BIODB.CHEBI.ID
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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33 MSDB.TAG.HMDB <- BIODB.HMDB.ID
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34 MSDB.TAG.KEGG <- BIODB.KEGG.ID
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36 # Mode tags
1
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37 MSDB.TAG.POS <- BIODB.MSMODE.NEG
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38 MSDB.TAG.NEG <- BIODB.MSMODE.POS
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40 # Fields containing multiple values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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41 MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES)
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42 MSDB.MULTIVAL.FIELD.SEP <- ';'
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44 # Authorized mz tolerance unit values
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45 MSDB.MZTOLUNIT.PPM <- 'ppm'
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46 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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47 MSDB.MZTOLUNIT.VALS <- c(MSDB.MZTOLUNIT.PPM, MSDB.MZTOLUNIT.PLAIN)
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49 # Default values
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50 MSDB.DFT.PREC <- list()
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51 MSDB.DFT.PREC[[MSDB.TAG.POS]] <- c("[(M+H)]+", "[M+H]+", "[(M+Na)]+", "[M+Na]+", "[(M+K)]+", "[M+K]+")
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52 MSDB.DFT.PREC[[MSDB.TAG.NEG]] <- c("[(M-H)]-", "[M-H]-", "[(M+Cl)]-", "[M+Cl]-")
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53 MSDB.DFT.OUTPUT.FIELDS <- list( mz = 'mz', rt = 'rt', col = 'col', colrt = 'colrt', molid = 'id', attr = 'attribution', comp = 'composition', int = 'intensity', rel = 'relative', mzexp = 'mzexp', mztheo = 'mztheo', msmatching = 'msmatching', molnames = 'molnames', molcomp = 'molcomp', molmass = 'molmass', inchi = 'inchi', inchikey = 'inchikey', pubchem = 'pubchem', chebi = 'chebi', hmdb = 'hmdb', kegg = 'kegg')
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54 MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP <- MSDB.MULTIVAL.FIELD.SEP
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55 MSDB.DFT.MATCH.FIELDS <- list( molids = 'molid', molnames = 'molnames')
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56 MSDB.DFT.MATCH.SEP <- ','
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57 MSDB.DFT.MODES <- list( pos = 'POS', neg = 'NEG')
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58 MSDB.DFT.MZTOLUNIT <- MSDB.MZTOLUNIT.PPM
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60 ############################
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61 # GET DEFAULT INPUT FIELDS #
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62 ############################
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64 msdb.get.dft.input.fields <- function () {
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66 dft.fields <- list()
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68 for(f in c(MSDB.TAG.MZ, MSDB.TAG.RT))
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69 dft.fields[[f]] <- f
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71 return(dft.fields)
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72 }
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74 #############################
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75 # GET DEFAULT OUTPUT FIELDS #
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76 #############################
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78 msdb.get.dft.output.fields <- function () {
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80 dft.fields <- list()
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82 for(f in c(MSDB.TAG.MZ, MSDB.TAG.RT, MSDB.TAG.COL, MSDB.TAG.COLRT, MSDB.TAG.MOLID, MSDB.TAG.ATTR, MSDB.TAG.COMP, MSDB.TAG.INT, MSDB.TAG.REL, MSDB.TAG.MZEXP, MSDB.TAG.MZTHEO, 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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83 dft.fields[[f]] <- f
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84
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85 return(dft.fields)
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86 }
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88 #########################
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89 # GET DEFAULT DB FIELDS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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90 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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91
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92 msdb.get.dft.db.fields <- function () {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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93
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94 dft.fields <- list()
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95
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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96 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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97 dft.fields[[f]] <- f
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98
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99 return(dft.fields)
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100 }
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101
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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102 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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103 # MAKE DB FIELDS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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104 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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105
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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106 msdb.make.db.fields <- function(fields) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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107
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108 # Merge with default fields
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109 dft.fields <- msdb.get.dft.db.fields()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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110 absent <- ! names(dft.fields) %in% names(fields)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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111 if (length(absent) > 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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112 fields <- c(fields, dft.fields[absent])
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113
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114 return(fields)
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115 }
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116
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117 #########################
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118 # MAKE INPUT DATA FRAME #
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119 #########################
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120
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121 msdb.make.input.df <- function(mz, rt = NULL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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122
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123 field <- msdb.get.dft.input.fields()
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124
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125 x <- data.frame()
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126
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127 # Set mz
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128 if (length(mz) > 1)
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129 x[seq(mz), field[[MSDB.TAG.MZ]]] <- mz
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130 else if (length(mz) == 1)
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131 x[1, field[[MSDB.TAG.MZ]]] <- mz
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132 else
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133 x[, field[[MSDB.TAG.MZ]]] <- numeric()
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134
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135 # Set rt
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136 if ( ! is.null(rt)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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137 if (length(rt) > 1)
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138 x[seq(rt), field[[MSDB.TAG.RT]]] <- rt
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139 else if (length(rt) == 1)
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140 x[1, field[[MSDB.TAG.RT]]] <- rt
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141 else
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142 x[, field[[MSDB.TAG.RT]]] <- numeric()
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143 }
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144
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145 return(x)
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146 }
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147
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148 ###############################
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149 # GET EMPTY RESULT DATA FRAME #
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150 ###############################
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151
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152 .get.empty.result.df <- function(rt = FALSE) {
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153
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154 df <- data.frame(stringsAsFactors = FALSE)
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155 df[MSDB.TAG.MOLID] <- character()
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156 df[MSDB.TAG.MOLNAMES] <- character()
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157 df[MSDB.TAG.MZ] <- numeric()
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158 df[MSDB.TAG.MZTHEO] <- numeric()
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159 df[MSDB.TAG.ATTR] <- character()
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160 df[MSDB.TAG.COMP] <- character()
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161 if (rt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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162 df[MSDB.TAG.RT] <- numeric()
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163 df[MSDB.TAG.COL] <- character()
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164 df[MSDB.TAG.COLRT] <- numeric()
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165 }
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166
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167 return(df)
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168 }
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169
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170 ############################
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171 # PARSE COLUMN DESCRIPTION #
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172 ############################
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173
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174 .parse_chrom_col_desc <- function(desc) {
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175
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176 # Clean string
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177 s <- desc
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178 s <- gsub('\\.+', ' ', s, perl = TRUE) # Replace '.' characters by spaces
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179 s <- gsub('[*-]', ' ', s, perl = TRUE) # Replace dashes and asterisks by spaces
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180 s <- gsub('[)(]', '', s, perl = TRUE) # Remove paranthesis
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181 s <- trim(s)
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182 s <- tolower(s) # put in lowercase
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183
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184 # Match 2 3 4 5 6 7 8 9 10 1112 13
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185 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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186 g <- str_match(s, pattern)
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187 if (is.na(g[1, 1]))
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188 stop(paste0("Impossible to parse column description \"", desc, "\"."))
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189
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190 type <- g[1, 2]
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191 stationary_phase <- if ( ! is.na(g[1, 4]) && nchar(g[1, 4]) > 0) g[1, 4] else NA_character_
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192 msdevice <- if ( ! is.na(g[1, 8]) && nchar(g[1, 8]) > 0) g[1, 8] else NA_character_
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193 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_ )
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194
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195 # Correct values
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196 if ( ! is.na(stationary_phase) && stationary_phase == '150 5 2 1') stationary_phase <- '150*5*2.1'
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197 if ( ! is.na(msdevice)) msdevice <- gsub(' ', '', msdevice) # remove spaces
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198
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199 return(list( type = type, stationary_phase = stationary_phase, time = time, msdevice = msdevice))
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200
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201 }
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202
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203 #########################
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204 # NORMALIZE COLUMN NAME #
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205 #########################
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206
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207 .normalize_column_name <- function(desc) {
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208
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209 lst <- .parse_chrom_col_desc(desc)
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210
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211 v <- c(lst$type)
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212 if ( ! is.na(lst$stationary_phase))
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213 v <- c(v, lst$stationary_phase)
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214 if ( ! is.na(lst$time))
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215 v <- c(v, paste0(lst$time, "min"))
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216 if ( ! is.na(lst$msdevice))
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217 v <- c(v, lst$msdevice)
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218
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219 return(paste(v, collapse = '-'))
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220 }
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221
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222 } # end of load safe guard