Mercurial > repos > tomnl > mspurity_createdatabase

comparison spectralMatching.R @ 0:f075f67c7416 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 08:59:45 -0400
parents
children c34cdaca2fcb
comparison
equal deleted inserted replaced
-1:000000000000 0:f075f67c7416
1 library(msPurity)
2 library(msPurityData)
3 library(optparse)
4 print(sessionInfo())
5
6
7 option_list <- list(
8 make_option(c("-o", "--outDir"), type="character"),
9 make_option("--q_dbPth", type="character"),
10 make_option("--l_dbPth", type="character"),
11
12 make_option("--q_msp", type="character", default=NA),
13 make_option("--l_msp", type="character", default=NA),
14
15 make_option("--q_defaultDb", action="store_true"),
16 make_option("--l_defaultDb", action="store_true"),
17
18 make_option("--q_ppmPrec", type="double"),
19 make_option("--l_ppmPrec", type="double"),
20
21 make_option("--q_ppmProd", type="double"),
22 make_option("--l_ppmProd", type="double"),
23
24 make_option("--q_raThres", type="double", default=NA),
25 make_option("--l_raThres", type="double", default=NA),
26
27 make_option("--q_polarity", type="character", default=NA),
28 make_option("--l_polarity", type="character", default=NA),
29
30 make_option("--q_purity", type="double", default=NA),
31 make_option("--l_purity", type="double", default=NA),
32
33 make_option("--q_xcmsGroups", type="character", default=NA),
34 make_option("--l_xcmsGroups", type="character", default=NA),
35
36 make_option("--q_pids", type="character", default=NA),
37 make_option("--l_pids", type="character", default=NA),
38
39 make_option("--q_rtrangeMin", type="double", default=NA),
40 make_option("--l_rtrangeMin", type="double", default=NA),
41
42 make_option("--q_rtrangeMax", type="double", default=NA),
43 make_option("--l_rtrangeMax", type="double", default=NA),
44
45 make_option("--q_accessions", type="character", default=NA),
46 make_option("--l_accessions", type="character", default=NA),
47
48 make_option("--q_sources", type="character", default=NA),
49 make_option("--l_sources", type="character", default=NA),
50
51 make_option("--q_sourcesUser", type="character", default=NA),
52 make_option("--l_sourcesUser", type="character", default=NA),
53
54 make_option("--q_instrumentTypes", type="character", default=NA),
55 make_option("--l_instrumentTypes", type="character", default=NA),
56
57 make_option("--q_instrumentTypesUser", type="character", default=NA),
58 make_option("--l_instrumentTypesUser", type="character", default=NA),
59
60 make_option("--q_instruments", type="character", default=NA),
61 make_option("--l_instruments", type="character", default=NA),
62
63 make_option("--q_spectraTypes", type="character", default=NA),
64 make_option("--l_spectraTypes", type="character", default=NA),
65
66 make_option("--q_spectraFilter", action="store_true"),
67 make_option("--l_spectraFilter", action="store_true"),
68
69 make_option("--usePrecursors", action="store_true"),
70
71 make_option("--mzW", type="double"),
72 make_option("--raW", type="double"),
73
74 make_option("--rttol", type="double", default=NA),
75
76 make_option("--updateDb", action="store_true"),
77 make_option("--copyDb", action="store_true"),
78 make_option("--cores", default=1)
79
80
81 )
82
83 # store options
84 opt<- parse_args(OptionParser(option_list=option_list))
85
86 print(opt)
87
88 extractMultiple <- function(optParam){
89 if (!is.na(optParam)){
90 param <- trimws(strsplit(optParam, ',')[[1]])
91 param <- param[param != ""]
92 }else{
93 param <- NA
94 }
95 return(param)
96
97 }
98
99 if(!is.null(opt$q_defaultDb)){
100 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
101 }else if (!is.null(opt$q_dbPth)){
102 q_dbPth <- opt$q_dbPth
103 }else{
104 message('No query database available')
105 exit()
106 }
107
108 if(!is.null(opt$l_defaultDb)){
109 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
110 }else if (!is.null(opt$l_dbPth)){
111 l_dbPth <- opt$l_dbPth
112 }else{
113 message('No library database available')
114 exit()
115 }
116
117
118 q_polarity <- extractMultiple(opt$q_polarity)
119 l_polarity <- extractMultiple(opt$l_polarity)
120
121 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)
122 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)
123
124 q_pids <- extractMultiple(opt$q_pids)
125 l_pids <- extractMultiple(opt$l_pids)
126
127 q_sources <- extractMultiple(opt$q_sources)
128 l_sources <- extractMultiple(opt$l_sources)
129
130 q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
131 l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
132
133 q_sources <-c(q_sources, q_sourcesUser)
134 l_sources <-c(l_sources, l_sourcesUser)
135
136 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
137 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
138
139 q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)
140 l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)
141
142
143 if(!is.null(opt$l_spectraFilter)){
144 l_spectraFilter <- TRUE
145 }else{
146 l_spectraFilter <- FALSE
147 }
148
149 if(!is.null(opt$q_spectraFilter)){
150 q_spectraFilter <- TRUE
151 }else{
152 q_spectraFilter <- FALSE
153 }
154
155 if(!is.null(opt$updateDb)){
156 updateDb <- TRUE
157 }else{
158 updateDb <- FALSE
159 }
160
161 if(!is.null(opt$copyDb)){
162 copyDb <- TRUE
163 }else{
164 copyDb <- FALSE
165 }
166
167 if(!is.null(opt$l_rtrangeMax)){
168 l_rtrangeMax <- opt$l_rtrangeMax
169 }else{
170 l_rtrangeMax <- NA
171 }
172
173 if(!is.null(opt$q_rtrangeMax)){
174 q_rtrangeMax <- opt$q_rtrangeMax
175 }else{
176 q_rtrangeMax <- NA
177 }
178
179 if(!is.null(opt$l_rtrangeMin)){
180 l_rtrangeMin <- opt$l_rtrangeMin
181 }else{
182 l_rtrangeMin <- NA
183 }
184
185 if(!is.null(opt$q_rtrangeMin)){
186 q_rtrangeMin <- opt$q_rtrangeMin
187 }else{
188 q_rtrangeMin <- NA
189 }
190
191
192
193 sm <- msPurity::spectralMatching(q_dbPth = q_dbPth,
194 l_dbPth = l_dbPth,
195
196 q_purity = opt$q_purity,
197 l_purity = opt$l_purity,
198
199 q_ppmProd = opt$q_ppmProd,
200 l_ppmProd = opt$l_ppmProd,
201
202 q_ppmPrec = opt$q_ppmPrec,
203 l_ppmPrec = opt$l_ppmPrec,
204
205 q_raThres = opt$q_raThres,
206 l_raThres = opt$l_raThres,
207
208 q_pol = q_polarity,
209 l_pol = l_polarity,
210
211 q_xcmsGroups = q_xcmsGroups,
212 l_xcmsGroups = l_xcmsGroups,
213
214 q_pids = q_pids,
215 l_pids = l_pids,
216
217 q_sources = q_sources,
218 l_sources = l_sources,
219
220 q_instrumentTypes = q_instrumentTypes,
221 l_instrumentTypes = l_instrumentTypes,
222
223 q_spectraFilter= q_spectraFilter,
224 l_spectraFilter= l_spectraFilter,
225
226 l_rtrange=c(l_rtrangeMin, l_rtrangeMax),
227 q_rtrange=c(q_rtrangeMin, q_rtrangeMax),
228
229 q_accessions = opt$q_accessions,
230 l_accessions= opt$l_accessions,
231
232 raW = opt$raW,
233 mzW = opt$mzW,
234 rttol=opt$rttol,
235 cores=opt$cores,
236
237 copyDb=copyDb,
238 updateDb=updateDb,
239 outPth = "db_with_spectral_matching.sqlite"
240 )
241
242
243
244 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
245 write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)