Mercurial > repos > computational-metabolomics > mspurity_createdatabase
comparison spectralMatching.R @ 6:2f71b3495221 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
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date | Thu, 04 Mar 2021 12:27:21 +0000 |
parents | 3d36a391612c |
children |
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5:3ec6fd8e4c17 | 6:2f71b3495221 |
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1 library(msPurity) | 1 library(msPurity) |
2 library(msPurityData) | 2 library(msPurityData) |
3 library(optparse) | 3 library(optparse) |
4 print(sessionInfo()) | 4 print(sessionInfo()) |
5 # load in library spectra config | 5 # load in library spectra config |
6 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } | 6 source_local <- function(fname) { |
7 argv <- commandArgs(trailingOnly = FALSE) | |
8 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
9 source(paste(base_dir, fname, sep = "/")) | |
10 } | |
7 source_local("dbconfig.R") | 11 source_local("dbconfig.R") |
8 | 12 |
9 option_list <- list( | 13 option_list <- list( |
10 make_option(c("-o", "--outDir"), type="character"), | 14 make_option(c("-o", "--outDir"), type = "character"), |
11 make_option("--q_dbPth", type="character"), | 15 make_option("--q_dbPth", type = "character"), |
12 make_option("--l_dbPth", type="character"), | 16 make_option("--l_dbPth", type = "character"), |
13 | 17 |
14 make_option("--q_dbType", type="character", default=NA), | 18 make_option("--q_dbType", type = "character", default = NA), |
15 make_option("--l_dbType", type="character", default=NA), | 19 make_option("--l_dbType", type = "character", default = NA), |
16 | 20 |
17 make_option("--q_msp", type="character", default=NA), | 21 make_option("--q_msp", type = "character", default = NA), |
18 make_option("--l_msp", type="character", default=NA), | 22 make_option("--l_msp", type = "character", default = NA), |
19 | 23 |
20 make_option("--q_defaultDb", action="store_true"), | 24 make_option("--q_defaultDb", action = "store_true"), |
21 make_option("--l_defaultDb", action="store_true"), | 25 make_option("--l_defaultDb", action = "store_true"), |
22 | 26 |
23 make_option("--q_ppmPrec", type="double"), | 27 make_option("--q_ppmPrec", type = "double"), |
24 make_option("--l_ppmPrec", type="double"), | 28 make_option("--l_ppmPrec", type = "double"), |
25 | 29 |
26 make_option("--q_ppmProd", type="double"), | 30 make_option("--q_ppmProd", type = "double"), |
27 make_option("--l_ppmProd", type="double"), | 31 make_option("--l_ppmProd", type = "double"), |
28 | 32 |
29 make_option("--q_raThres", type="double", default=NA), | 33 make_option("--q_raThres", type = "double", default = NA), |
30 make_option("--l_raThres", type="double", default=NA), | 34 make_option("--l_raThres", type = "double", default = NA), |
31 | 35 |
32 make_option("--q_polarity", type="character", default=NA), | 36 make_option("--q_polarity", type = "character", default = NA), |
33 make_option("--l_polarity", type="character", default=NA), | 37 make_option("--l_polarity", type = "character", default = NA), |
34 | 38 |
35 make_option("--q_purity", type="double", default=NA), | 39 make_option("--q_purity", type = "double", default = NA), |
36 make_option("--l_purity", type="double", default=NA), | 40 make_option("--l_purity", type = "double", default = NA), |
37 | 41 |
38 make_option("--q_xcmsGroups", type="character", default=NA), | 42 make_option("--q_xcmsGroups", type = "character", default = NA), |
39 make_option("--l_xcmsGroups", type="character", default=NA), | 43 make_option("--l_xcmsGroups", type = "character", default = NA), |
40 | 44 |
41 make_option("--q_pids", type="character", default=NA), | 45 make_option("--q_pids", type = "character", default = NA), |
42 make_option("--l_pids", type="character", default=NA), | 46 make_option("--l_pids", type = "character", default = NA), |
43 | 47 |
44 make_option("--q_rtrangeMin", type="double", default=NA), | 48 make_option("--q_rtrangeMin", type = "double", default = NA), |
45 make_option("--l_rtrangeMin", type="double", default=NA), | 49 make_option("--l_rtrangeMin", type = "double", default = NA), |
46 | 50 |
47 make_option("--q_rtrangeMax", type="double", default=NA), | 51 make_option("--q_rtrangeMax", type = "double", default = NA), |
48 make_option("--l_rtrangeMax", type="double", default=NA), | 52 make_option("--l_rtrangeMax", type = "double", default = NA), |
49 | 53 |
50 make_option("--q_accessions", type="character", default=NA), | 54 make_option("--q_accessions", type = "character", default = NA), |
51 make_option("--l_accessions", type="character", default=NA), | 55 make_option("--l_accessions", type = "character", default = NA), |
52 | 56 |
53 make_option("--q_sources", type="character", default=NA), | 57 make_option("--q_sources", type = "character", default = NA), |
54 make_option("--l_sources", type="character", default=NA), | 58 make_option("--l_sources", type = "character", default = NA), |
55 | 59 |
56 make_option("--q_sourcesUser", type="character", default=NA), | 60 make_option("--q_sourcesUser", type = "character", default = NA), |
57 make_option("--l_sourcesUser", type="character", default=NA), | 61 make_option("--l_sourcesUser", type = "character", default = NA), |
58 | 62 |
59 make_option("--q_instrumentTypes", type="character", default=NA), | 63 make_option("--q_instrumentTypes", type = "character", default = NA), |
60 make_option("--l_instrumentTypes", type="character", default=NA), | 64 make_option("--l_instrumentTypes", type = "character", default = NA), |
61 | 65 |
62 make_option("--q_instrumentTypesUser", type="character", default=NA), | 66 make_option("--q_instrumentTypesUser", type = "character", default = NA), |
63 make_option("--l_instrumentTypesUser", type="character", default=NA), | 67 make_option("--l_instrumentTypesUser", type = "character", default = NA), |
64 | 68 |
65 make_option("--q_instruments", type="character", default=NA), | 69 make_option("--q_instruments", type = "character", default = NA), |
66 make_option("--l_instruments", type="character", default=NA), | 70 make_option("--l_instruments", type = "character", default = NA), |
67 | 71 |
68 make_option("--q_spectraTypes", type="character", default=NA), | 72 make_option("--q_spectraTypes", type = "character", default = NA), |
69 make_option("--l_spectraTypes", type="character", default=NA), | 73 make_option("--l_spectraTypes", type = "character", default = NA), |
70 | 74 |
71 make_option("--q_spectraFilter", action="store_true"), | 75 make_option("--q_spectraFilter", action = "store_true"), |
72 make_option("--l_spectraFilter", action="store_true"), | 76 make_option("--l_spectraFilter", action = "store_true"), |
73 | 77 |
74 make_option("--usePrecursors", action="store_true"), | 78 make_option("--usePrecursors", action = "store_true"), |
75 | 79 |
76 make_option("--mzW", type="double"), | 80 make_option("--mzW", type = "double"), |
77 make_option("--raW", type="double"), | 81 make_option("--raW", type = "double"), |
78 | 82 |
79 make_option("--rttol", type="double", default=NA), | 83 make_option("--rttol", type = "double", default = NA), |
80 | 84 |
81 make_option("--updateDb", action="store_true"), | 85 make_option("--updateDb", action = "store_true"), |
82 make_option("--copyDb", action="store_true"), | 86 make_option("--copyDb", action = "store_true"), |
83 make_option("--cores", default=1) | 87 make_option("--cores", default = 1) |
84 | 88 |
85 | 89 |
86 ) | 90 ) |
87 | 91 |
88 # store options | 92 # store options |
89 opt<- parse_args(OptionParser(option_list=option_list)) | 93 opt <- parse_args(OptionParser(option_list = option_list)) |
90 | 94 |
91 print(opt) | 95 print(opt) |
92 | 96 |
93 # check if the sqlite databases have any spectra | 97 # check if the sqlite databases have any spectra |
94 checkSPeakMeta <- function(dbPth, nme){ | 98 checkSPeakMeta <- function(dbPth, nme) { |
95 if(is.null(dbPth)){ | 99 if (is.null(dbPth)) { |
96 return(TRUE) | 100 return(TRUE) |
97 }else if ((file.exists(dbPth)) & (file.info(dbPth)$size>0)){ | 101 }else if ((file.exists(dbPth)) & (file.info(dbPth)$size > 0)) { |
98 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth) | 102 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth) |
99 if (DBI::dbExistsTable(con, "s_peak_meta")){ | 103 if (DBI::dbExistsTable(con, "s_peak_meta")) { |
100 spm <- DBI::dbGetQuery(con, 'SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1') | 104 spm <- DBI::dbGetQuery(con, "SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1") |
101 return(TRUE) | 105 return(TRUE) |
102 }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ | 106 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) { |
103 spm <- DBI::dbGetQuery(con, 'SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1') | 107 spm <- DBI::dbGetQuery(con, "SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1") |
104 return(TRUE) | 108 return(TRUE) |
105 }else{ | 109 }else{ |
106 print(paste("No spectra available for ",nme)) | 110 print(paste("No spectra available for ", nme)) |
107 return(FALSE) | 111 return(FALSE) |
108 } | 112 } |
109 }else{ | 113 }else{ |
110 print(paste("file empty or does not exist for", nme)) | 114 print(paste("file empty or does not exist for", nme)) |
111 return(FALSE) | 115 return(FALSE) |
112 } | 116 } |
113 | 117 |
114 | 118 |
115 } | 119 } |
116 | 120 |
117 | 121 |
118 addQueryNameColumn <- function(sm){ | 122 addQueryNameColumn <- function(sm) { |
119 if (is.null(sm$matchedResults) || length(sm$matchedResults)==1 || nrow(sm$matchedResults)==0){ | 123 if (is.null(sm$matchedResults) || length(sm$matchedResults) == 1 || nrow(sm$matchedResults) == 0) { |
120 return(sm) | 124 return(sm) |
121 } | 125 } |
122 | 126 |
123 con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) | 127 con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth) |
124 if (DBI::dbExistsTable(con, "s_peak_meta")){ | 128 if (DBI::dbExistsTable(con, "s_peak_meta")) { |
125 spm <- DBI::dbGetQuery(con, 'SELECT pid, name AS query_entry_name FROM s_peak_meta') | 129 spm <- DBI::dbGetQuery(con, "SELECT pid, name AS query_entry_name FROM s_peak_meta") |
126 }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ | 130 }else if (DBI::dbExistsTable(con, "library_spectra_meta")) { |
127 spm <- DBI::dbGetQuery(con, 'SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta') | 131 spm <- DBI::dbGetQuery(con, "SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta") |
128 } | 132 } |
129 print(sm$matchedResults) | 133 print(sm$matchedResults) |
130 if ('pid' %in% colnames(sm$matchedResults)){ | 134 if ("pid" %in% colnames(sm$matchedResults)) { |
131 sm$matchedResults <- merge(sm$matchedResults, spm, by.x='pid', by.y='pid') | 135 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "pid", by.y = "pid") |
132 }else{ | 136 }else{ |
133 sm$matchedResults <- merge(sm$matchedResults, spm, by.x='qpid', by.y='pid') | 137 sm$matchedResults <- merge(sm$matchedResults, spm, by.x = "qpid", by.y = "pid") |
134 } | 138 } |
135 | 139 |
136 print(sm$xcmsMatchedResults) | 140 print(sm$xcmsMatchedResults) |
137 if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults)==1 || nrow(sm$xcmsMatchedResults)==0){ | 141 if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults) == 1 || nrow(sm$xcmsMatchedResults) == 0) { |
138 return(sm) | 142 return(sm) |
139 }else{ | 143 }else{ |
140 if ('pid' %in% colnames(sm$xcmsMatchedResults)){ | 144 if ("pid" %in% colnames(sm$xcmsMatchedResults)) { |
141 sm$xcmsMatchedResults<- merge(sm$xcmsMatchedResults, spm, by.x='pid', by.y='pid') | 145 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "pid", by.y = "pid") |
142 }else{ | 146 }else{ |
143 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x='qpid', by.y='pid') | 147 sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x = "qpid", by.y = "pid") |
144 } | 148 } |
145 } | 149 } |
146 | 150 |
147 return(sm) | 151 return(sm) |
148 | 152 |
149 } | 153 } |
150 | 154 |
151 | 155 |
152 updateDbF <- function(q_con, l_con){ | 156 updateDbF <- function(q_con, l_con) { |
153 message('Adding extra details to database') | 157 message("Adding extra details to database") |
154 q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) | 158 q_con <- DBI::dbConnect(RSQLite::SQLite(), sm$q_dbPth) |
155 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){ | 159 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")) { |
156 l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT * FROM l_s_peak_meta') | 160 l_s_peak_meta <- DBI::dbGetQuery(q_con, "SELECT * FROM l_s_peak_meta") |
157 colnames(l_s_peak_meta)[1] <- 'pid' | 161 colnames(l_s_peak_meta)[1] <- "pid" |
158 } | 162 } |
159 | 163 |
160 l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth) | 164 l_con <- DBI::dbConnect(RSQLite::SQLite(), l_dbPth) |
161 if (DBI::dbExistsTable(l_con, "s_peaks")){ | 165 if (DBI::dbExistsTable(l_con, "s_peaks")) { |
162 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) | 166 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ","))) |
163 | 167 |
164 }else if(DBI::dbExistsTable(l_con, "library_spectra")){ | 168 }else if (DBI::dbExistsTable(l_con, "library_spectra")) { |
165 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra | 169 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra |
166 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) | 170 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse = ","))) |
167 }else{ | 171 }else{ |
168 l_s_peaks = NULL | 172 l_s_peaks <- NULL |
169 } | 173 } |
170 | 174 |
171 if (DBI::dbExistsTable(l_con, "source")){ | 175 if (DBI::dbExistsTable(l_con, "source")) { |
172 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM source') | 176 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM source") |
173 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) { | 177 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) { |
174 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM library_spectra_source') | 178 l_source <- DBI::dbGetQuery(l_con, "SELECT * FROM library_spectra_source") |
175 }else{ | 179 }else{ |
176 l_source = NULL | 180 l_source <- NULL |
177 } | 181 } |
178 | 182 |
179 if (!is.null(l_s_peaks)){ | 183 if (!is.null(l_s_peaks)) { |
180 DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE) | 184 DBI::dbWriteTable(q_con, name = "l_s_peaks", value = l_s_peaks, row.names = FALSE, append = TRUE) |
181 } | 185 } |
182 | 186 |
183 if (!is.null(l_source)){ | 187 if (!is.null(l_source)) { |
184 DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE) | 188 DBI::dbWriteTable(q_con, name = "l_source", value = l_source, row.names = FALSE, append = TRUE) |
185 } | 189 } |
186 | 190 |
187 | 191 } |
188 } | 192 |
189 | 193 |
190 | 194 extractMultiple <- function(optParam) { |
191 extractMultiple <- function(optParam){ | 195 if (!is.na(optParam)) { |
192 if (!is.na(optParam)){ | 196 param <- trimws(strsplit(optParam, ",")[[1]]) |
193 param <- trimws(strsplit(optParam, ',')[[1]]) | |
194 param <- param[param != ""] | 197 param <- param[param != ""] |
195 }else{ | 198 }else { |
196 param <- NA | 199 param <- NA |
197 } | 200 } |
198 return(param) | 201 return(param) |
199 | 202 |
200 } | 203 } |
201 | 204 |
202 if(!is.null(opt$q_defaultDb)){ | 205 if (!is.null(opt$q_defaultDb)) { |
203 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") | 206 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData") |
204 q_dbType <- 'sqlite' | 207 q_dbType <- "sqlite" |
205 }else if (!opt$q_dbType=='local_config'){ | 208 }else if (!opt$q_dbType == "local_config") { |
206 q_dbType <- opt$q_dbType | 209 q_dbType <- opt$q_dbType |
207 q_dbPth <- opt$q_dbPth | 210 q_dbPth <- opt$q_dbPth |
208 } | 211 } |
209 | 212 |
210 if(!is.null(opt$l_defaultDb)){ | 213 if (!is.null(opt$l_defaultDb)) { |
211 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") | 214 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package = "msPurityData") |
212 l_dbType <- 'sqlite' | 215 l_dbType <- "sqlite" |
213 }else if (!opt$l_dbType=='local_config'){ | 216 }else if (!opt$l_dbType == "local_config") { |
214 l_dbType <- opt$l_dbType | 217 l_dbType <- opt$l_dbType |
215 l_dbPth <- opt$l_dbPth | 218 l_dbPth <- opt$l_dbPth |
216 } | 219 } |
217 | 220 |
221 q_spectraTypes <- extractMultiple(opt$q_spectraTypes) | |
222 l_spectraTypes <- extractMultiple(opt$l_spectraTypes) | |
218 | 223 |
219 q_polarity <- extractMultiple(opt$q_polarity) | 224 q_polarity <- extractMultiple(opt$q_polarity) |
220 l_polarity <- extractMultiple(opt$l_polarity) | 225 l_polarity <- extractMultiple(opt$l_polarity) |
221 | 226 |
222 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups) | 227 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups) |
229 l_sources <- extractMultiple(opt$l_sources) | 234 l_sources <- extractMultiple(opt$l_sources) |
230 | 235 |
231 q_sourcesUser <- extractMultiple(opt$q_sourcesUser) | 236 q_sourcesUser <- extractMultiple(opt$q_sourcesUser) |
232 l_sourcesUser <- extractMultiple(opt$l_sourcesUser) | 237 l_sourcesUser <- extractMultiple(opt$l_sourcesUser) |
233 | 238 |
234 q_sources <-c(q_sources, q_sourcesUser) | 239 q_sources <- c(q_sources, q_sourcesUser) |
235 l_sources <-c(l_sources, l_sourcesUser) | 240 l_sources <- c(l_sources, l_sourcesUser) |
236 | 241 |
237 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes) | 242 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes) |
238 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes) | 243 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes) |
239 | 244 |
240 q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes) | 245 q_instrumentTypes <- c(q_instrumentTypes, q_instrumentTypes) |
241 l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes) | 246 l_instrumentTypes <- c(l_instrumentTypes, l_instrumentTypes) |
242 | 247 |
243 | 248 |
244 if(!is.null(opt$l_spectraFilter)){ | 249 if (!is.null(opt$l_spectraFilter)) { |
245 l_spectraFilter <- TRUE | 250 l_spectraFilter <- TRUE |
246 }else{ | 251 }else{ |
247 l_spectraFilter <- FALSE | 252 l_spectraFilter <- FALSE |
248 } | 253 } |
249 | 254 |
250 if(!is.null(opt$q_spectraFilter)){ | 255 if (!is.null(opt$q_spectraFilter)) { |
251 q_spectraFilter <- TRUE | 256 q_spectraFilter <- TRUE |
252 }else{ | 257 }else{ |
253 q_spectraFilter <- FALSE | 258 q_spectraFilter <- FALSE |
254 } | 259 } |
255 | 260 |
256 if(!is.null(opt$updateDb)){ | 261 if (!is.null(opt$updateDb)) { |
257 updateDb <- TRUE | 262 updateDb <- TRUE |
258 }else{ | 263 }else{ |
259 updateDb <- FALSE | 264 updateDb <- FALSE |
260 } | 265 } |
261 | 266 |
262 if(!is.null(opt$copyDb)){ | 267 if (!is.null(opt$copyDb)) { |
263 copyDb <- TRUE | 268 copyDb <- TRUE |
264 }else{ | 269 }else{ |
265 copyDb <- FALSE | 270 copyDb <- FALSE |
266 } | 271 } |
267 | 272 |
268 if(!is.null(opt$l_rtrangeMax)){ | 273 if (!is.null(opt$l_rtrangeMax)) { |
269 l_rtrangeMax <- opt$l_rtrangeMax | 274 l_rtrangeMax <- opt$l_rtrangeMax |
270 }else{ | 275 }else{ |
271 l_rtrangeMax <- NA | 276 l_rtrangeMax <- NA |
272 } | 277 } |
273 | 278 |
274 if(!is.null(opt$q_rtrangeMax)){ | 279 if (!is.null(opt$q_rtrangeMax)) { |
275 q_rtrangeMax <- opt$q_rtrangeMax | 280 q_rtrangeMax <- opt$q_rtrangeMax |
276 }else{ | 281 }else{ |
277 q_rtrangeMax <- NA | 282 q_rtrangeMax <- NA |
278 } | 283 } |
279 | 284 |
280 if(!is.null(opt$l_rtrangeMin)){ | 285 if (!is.null(opt$l_rtrangeMin)) { |
281 l_rtrangeMin <- opt$l_rtrangeMin | 286 l_rtrangeMin <- opt$l_rtrangeMin |
282 }else{ | 287 }else{ |
283 l_rtrangeMin <- NA | 288 l_rtrangeMin <- NA |
284 } | 289 } |
285 | 290 |
286 if(!is.null(opt$q_rtrangeMin)){ | 291 if (!is.null(opt$q_rtrangeMin)) { |
287 q_rtrangeMin <- opt$q_rtrangeMin | 292 q_rtrangeMin <- opt$q_rtrangeMin |
288 }else{ | 293 }else{ |
289 q_rtrangeMin <- NA | 294 q_rtrangeMin <- NA |
290 } | 295 } |
291 | 296 |
292 q_check <- checkSPeakMeta(opt$q_dbPth, 'query') | 297 q_check <- checkSPeakMeta(opt$q_dbPth, "query") |
293 l_check <- checkSPeakMeta(opt$l_dbPth, 'library') | 298 l_check <- checkSPeakMeta(opt$l_dbPth, "library") |
294 | 299 |
295 | 300 |
296 if (q_check && l_check){ | 301 if (q_check && l_check) { |
297 sm <- msPurity::spectralMatching( | 302 sm <- msPurity::spectralMatching( |
298 q_purity = opt$q_purity, | 303 q_purity = opt$q_purity, |
299 l_purity = opt$l_purity, | 304 l_purity = opt$l_purity, |
300 | 305 |
301 q_ppmProd = opt$q_ppmProd, | 306 q_ppmProd = opt$q_ppmProd, |
302 l_ppmProd = opt$l_ppmProd, | 307 l_ppmProd = opt$l_ppmProd, |
303 | 308 |
304 q_ppmPrec = opt$q_ppmPrec, | 309 q_ppmPrec = opt$q_ppmPrec, |
305 l_ppmPrec = opt$l_ppmPrec, | 310 l_ppmPrec = opt$l_ppmPrec, |
306 | 311 |
307 q_raThres = opt$q_raThres, | 312 q_raThres = opt$q_raThres, |
308 l_raThres = opt$l_raThres, | 313 l_raThres = opt$l_raThres, |
309 | 314 |
310 q_pol = q_polarity, | 315 q_pol = q_polarity, |
311 l_pol = l_polarity, | 316 l_pol = l_polarity, |
312 | 317 |
318 q_spectraFilter = q_spectraFilter, | |
319 l_spectraFilter = l_spectraFilter, | |
320 | |
313 q_xcmsGroups = q_xcmsGroups, | 321 q_xcmsGroups = q_xcmsGroups, |
314 l_xcmsGroups = l_xcmsGroups, | 322 l_xcmsGroups = l_xcmsGroups, |
315 | 323 |
316 q_pids = q_pids, | 324 q_pids = q_pids, |
317 l_pids = l_pids, | 325 l_pids = l_pids, |
318 | 326 |
319 q_sources = q_sources, | 327 q_sources = q_sources, |
320 l_sources = l_sources, | 328 l_sources = l_sources, |
321 | 329 |
322 q_instrumentTypes = q_instrumentTypes, | 330 q_instrumentTypes = q_instrumentTypes, |
323 l_instrumentTypes = l_instrumentTypes, | 331 l_instrumentTypes = l_instrumentTypes, |
324 | 332 |
325 q_spectraFilter= q_spectraFilter, | 333 q_spectraTypes = q_spectraTypes, |
326 l_spectraFilter= l_spectraFilter, | 334 l_spectraTypes = l_spectraTypes, |
327 | 335 |
328 l_rtrange=c(l_rtrangeMin, l_rtrangeMax), | 336 l_rtrange = c(l_rtrangeMin, l_rtrangeMax), |
329 q_rtrange=c(q_rtrangeMin, q_rtrangeMax), | 337 q_rtrange = c(q_rtrangeMin, q_rtrangeMax), |
330 | 338 |
331 q_accessions = opt$q_accessions, | 339 q_accessions = opt$q_accessions, |
332 l_accessions= opt$l_accessions, | 340 l_accessions = opt$l_accessions, |
333 | 341 |
334 raW = opt$raW, | 342 raW = opt$raW, |
335 mzW = opt$mzW, | 343 mzW = opt$mzW, |
336 rttol=opt$rttol, | 344 rttol = opt$rttol, |
337 cores=opt$cores, | 345 cores = opt$cores, |
338 | 346 |
339 copyDb=copyDb, | 347 copyDb = copyDb, |
340 updateDb=updateDb, | 348 updateDb = updateDb, |
341 outPth = "db_with_spectral_matching.sqlite", | 349 outPth = "db_with_spectral_matching.sqlite", |
342 | 350 |
343 q_dbPth = q_dbPth, | 351 q_dbPth = q_dbPth, |
344 q_dbType = q_dbType, | 352 q_dbType = q_dbType, |
345 q_dbName = q_dbName, | 353 q_dbName = q_dbName, |
346 q_dbHost = q_dbHost, | 354 q_dbHost = q_dbHost, |
347 q_dbUser = q_dbUser, | 355 q_dbUser = q_dbUser, |
348 q_dbPass = q_dbPass, | 356 q_dbPass = q_dbPass, |
349 q_dbPort = q_dbPort, | 357 q_dbPort = q_dbPort, |
350 | 358 |
351 l_dbPth = l_dbPth, | 359 l_dbPth = l_dbPth, |
352 l_dbType = l_dbType, | 360 l_dbType = l_dbType, |
353 l_dbName = l_dbName, | 361 l_dbName = l_dbName, |
354 l_dbHost = l_dbHost, | 362 l_dbHost = l_dbHost, |
355 l_dbUser = l_dbUser, | 363 l_dbUser = l_dbUser, |
356 l_dbPass = l_dbPass, | 364 l_dbPass = l_dbPass, |
357 l_dbPort = l_dbPort | 365 l_dbPort = l_dbPort |
358 | 366 |
359 ) | 367 ) |
360 | 368 |
361 sm <- addQueryNameColumn(sm) | 369 sm <- addQueryNameColumn(sm) |
362 # Get name of the query results (and merged with the data frames) | 370 # Get name of the query results (and merged with the data frames) |
363 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) | 371 write.table(sm$matchedResults, "matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE) |
364 write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) | 372 write.table(sm$xcmsMatchedResults, "xcms_matched_results.tsv", sep = "\t", row.names = FALSE, col.names = TRUE) |
365 | 373 |
366 if(updateDb){ | 374 if (updateDb) { |
367 updateDbF(q_con, l_con) | 375 updateDbF(q_con, l_con) |
368 } | 376 } |
369 } | 377 } |