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comparison search-mz @ 6:f86fec07f392 draft default tip

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planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce
author prog
date Fri, 22 Feb 2019 16:04:22 -0500
parents fb9c0409d85c
children
comparison
equal deleted inserted replaced
5:fb9c0409d85c 6:f86fec07f392
1 #!/usr/bin/env Rscript
2 # vi: ft=R fdm=marker
3 args <- commandArgs(trailingOnly = F)
4 script.path <- sub("--file=","",args[grep("--file=",args)])
5 library(getopt)
6 source(file.path(dirname(script.path), 'msdb-common.R'), chdir = TRUE)
7 source(file.path(dirname(script.path), 'MsDbLogger.R'), chdir = TRUE)
8 source(file.path(dirname(script.path), 'MsDbInputDataFrameStream.R'), chdir = TRUE)
9 source(file.path(dirname(script.path), 'MsDbOutputDataFrameStream.R'), chdir = TRUE)
10 source(file.path(dirname(script.path), 'htmlhlp.R'), chdir = TRUE)
11 source(file.path(dirname(script.path), 'strhlp.R'), chdir = TRUE)
12 source(file.path(dirname(script.path), 'fshlp.R'), chdir = TRUE)
13 source(file.path(dirname(script.path), 'biodb-common.R'), chdir = TRUE)
14 source(file.path(dirname(script.path), 'nethlp.R'), chdir = TRUE)
15
16 # Missing paste0() function in R 2.14.1
17 if (as.integer(R.Version()$major) == 2 && as.numeric(R.Version()$minor) < 15)
18 paste0 <- function(...) paste(..., sep = '')
19
20 # Constants {{{1
21 ################################################################
22
23 PROG <- sub('^.*/([^/]+)$', '\\1', commandArgs()[4], perl = TRUE)
24 USERAGENT <- 'search-mz ; pierrick.roger@gmail.com'
25
26 # Authorized database types
27 MSDB.XLS <- 'xls'
28 MSDB.4TABSQL <- '4tabsql'
29 MSDB.FILE <- 'file'
30 MSDB.PEAKFOREST <- 'peakforest'
31 MSDB.VALS <- c(MSDB.XLS, MSDB.4TABSQL, MSDB.FILE, MSDB.PEAKFOREST)
32 DB.SRC.FILE <- list ()
33 DB.SRC.FILE[[MSDB.FILE]] <- 'MsFileDb.R'
34 DB.SRC.FILE[[MSDB.PEAKFOREST]] <- 'MsPeakForestDb.R'
35 DB.SRC.FILE[[MSDB.XLS]] <- 'MsXlsDb.R'
36 DB.SRC.FILE[[MSDB.4TABSQL]] <- 'Ms4TabSqlDb.R'
37
38 # Authorized mode values
39 POS_MODE <- 'pos'
40 NEG_MODE <- 'neg'
41 MSDB.MODE.VALS <- c(POS_MODE, NEG_MODE)
42
43 # Default
44 MSDB.DFT <- list()
45 MSDB.DFT[['mzshift']] <- 0 # in ppm
46 MSDB.DFT[['mzprec']] <- 5 # in ppm
47 MSDB.DFT[['mztolunit']] <- MSDB.DFT.MZTOLUNIT
48 MSDB.DFT[['precursor-rt-tol']] <- 5
49 MSDB.DFT[['molids-sep']] <- MSDB.DFT.MATCH.SEP
50 MSDB.DFT[['db-fields']] <- concat.kv.list(msdb.get.dft.db.fields())
51 MSDB.DFT[['db-ms-modes']] <- concat.kv.list(MSDB.DFT.MODES)
52 MSDB.DFT[['pos-prec']] <- paste(MSDB.DFT.PREC[[MSDB.TAG.POS]], collapse = ',')
53 MSDB.DFT[['neg-prec']] <- paste(MSDB.DFT.PREC[[MSDB.TAG.NEG]], collapse = ',')
54 MSDB.DFT[['db-rt-unit']] <- MSDB.RTUNIT.SEC
55 MSDB.DFT[['rtunit']] <- MSDB.RTUNIT.SEC
56 DEFAULT.ARG.VALUES <- MSDB.DFT
57 DEFAULT.ARG.VALUES[['input-col-names']] <- concat.kv.list(msdb.get.dft.input.fields())
58
59 # Print help {{{1
60 ################################################################
61
62 print.help <- function() {
63
64 cat("USAGE:\n")
65 prog.mz.match <- paste(PROG, ' -d (', paste(MSDB.VALS, collapse = '|'), ') --url (file|dir|database URL) -i <file> -m (', paste(MSDB.MODE.VALS, collapse = '|'), ") -p <mz precision> -s <mz shift> -u (", paste(MSDB.MZTOLUNIT.VALS, collapse = '|'), ") -o <file>", sep = '')
66 cat("\t(1) ", prog.mz.match, " ...\n", sep = '')
67 cat("\n")
68 cat("\t(2) ", prog.mz.match, "(--all-cols|-c <cols>) -x <X RT tolerance> -y <Y RT tolerance>", " ...\n", sep = '')
69 cat("\n")
70 cat("\t(3) ", PROG, ' -d (', paste(MSDB.VALS, collapse = '|'), ") --url (file|dir|database URL) --list-cols\n", sep = '')
71
72 cat("\nDETAILS:\n")
73 cat("Form (1) is for running an MZ match on a database.\n")
74 cat("Form (2) is for running an MZ/RT match on a database.\n")
75 cat("Form (3) is for getting a list of available chromatographic columns in a database.\n")
76
77 cat("\nOPTIONS:\n")
78 spec <- matrix(make.getopt.spec(), byrow = TRUE, ncol = 5)
79 max.length.opt.cols <- max(nchar(spec[,1])) + 1
80 sections <- list(database = "Database setting", input = "Input file", output = "Output files", mz = "M/Z matching", rt = "RT matching", precursor = "Precursor matching", misc = "Miscellaneous")
81 for (section in names(sections)) {
82 cat("\n\t", sections[[section]], ":\n", sep = '')
83 spec <- matrix(make.getopt.spec(section), byrow = TRUE, ncol = 5)
84 for (i in seq(nrow(spec))) {
85 opt <- ''
86 if ( ! is.na(spec[i,2]))
87 opt <- paste('-', spec[i,2], '|', sep = '')
88 opt <- paste(opt, '--', spec[i, 1], sep = '')
89 nb.space.padding <- max.length.opt.cols - nchar(opt) + 6
90 padding <- paste(rep(' ', nb.space.padding), sep = '')
91 cat("\t\t", opt, padding, "\t", spec[i, 5], "\n", sep = '')
92 }
93 }
94
95 cat("\nEXAMPLES:\n")
96
97 cat("\nSimple M/Z matching with a file database:\n")
98 cat("\t./", PROG, " -d file --url mydbfile.tsv -i input.tsv -m pos -o output.tsv\n", sep = '')
99
100 cat("\nFile database with M/Z tolerance:\n")
101 cat("\t./", PROG, " -d file --url mydbfile.tsv -i input.tsv -m pos -o output.tsv -p 0.5 -s 0\n", sep = '')
102
103 cat("\nFile database with M/Z tolerance unit:\n")
104 cat("\t./", PROG, " -d file --url mydbfile.tsv -i input.tsv -m pos -o output.tsv -p 1 -s 0.5 -u plain\n", sep = '')
105
106 cat("\nPeakforest database:\n")
107 cat("\t./", PROG, " -d peakforest --url https://rest.peakforest.org/ --db-token <your Peakforest token> -i input.tsv -m pos -o output.tsv\n", sep = '')
108 }
109
110 # Set default argument values {{{1
111 ################################################################
112
113 set.dft.arg.val <-function(opt) {
114
115 for (f in names(MSDB.DFT))
116 if (is.null(opt[[f]]))
117 opt[[f]] <- MSDB.DFT[[f]]
118
119 # Set default values
120 if ( opt$database == MSDB.XLS && ! is.null(opt$url) && is.null(opt[['cache-dir']]))
121 opt[['cache-dir']] <- file.path(opt$url, 'cache')
122
123 if ( ! is.null(opt$rtcol) && opt$rtcol == '')
124 opt$rtcol <- NULL
125
126 return(opt)
127 }
128
129 # Parse argument values {{{1
130 ################################################################
131
132 parse.arg.val <- function(opt) {
133
134 # Parse input column names
135 if ( ! is.null(opt[['db-fields']])) {
136 cust <- split.kv.list(opt[['db-fields']])
137 cust <- cust[cust != 'NA']
138 opt[['db-fields']] <- split.kv.list(MSDB.DFT[['db-fields']])
139 cust <- cust[names(cust) %in% names(opt[['db-fields']])]
140 opt[['db-fields']][names(cust)] <- cust
141 }
142
143 # Parse MS modes
144 if ( ! is.null(opt[['db-ms-modes']])) {
145 cust <- split.kv.list(opt[['db-ms-modes']])
146 opt[['db-ms-modes']] <- split.kv.list(MSDB.DFT[['db-ms-modes']])
147 opt[['db-ms-modes']][names(cust)] <- cust
148 }
149
150 # Parse retention time columns
151 if ( ! is.null(opt$rtcol))
152 opt$rtcol <- strsplit(opt$rtcol, ',')[[1]]
153
154 # Parse input column names
155 if (is.null(opt[['input-col-names']])) {
156 opt[['input-col-names']] <- msdb.get.dft.input.fields()
157 }
158 else {
159 custcols <- split.kv.list(opt[['input-col-names']])
160 custcols <- custcols[custcols != 'NA']
161 dftcols <- msdb.get.dft.input.fields()
162 opt[['input-col-names']] <- c(custcols, dftcols[ ! names(dftcols) %in% names(custcols)])
163 }
164
165 # Parse lists of precursors
166 if ( ! is.null(opt[['pos-prec']]))
167 opt[['pos-prec']] <- split.str(opt[['pos-prec']], unlist = TRUE)
168 if ( ! is.null(opt[['neg-prec']]))
169 opt[['neg-prec']] <- split.str(opt[['neg-prec']], unlist = TRUE)
170
171 return(opt)
172 }
173
174 # Make getopt specifications {{{1
175 ################################################################
176
177 make.getopt.spec <- function(sections = NULL) {
178
179 spec <- character(0)
180
181 if (is.null(sections) || 'input' %in% sections)
182 spec <- c(spec,
183 'input-file', 'i', 1, 'character', 'Set input file.',
184 'input-col-names', 'j', 1, 'character', paste0('Set the input column names. Default is "', DEFAULT.ARG.VALUES[['input-col-names']], '".')
185 )
186
187 if (is.null(sections) || 'mz' %in% sections)
188 spec <- c(spec,
189 'mode', 'm', 1, 'character', paste0('MS mode. Possible values are:', paste(MSDB.MODE.VALS, collapse = ", "), '.'),
190 'mzshift', 's', 1, 'numeric', paste0('Shift on m/z. Default is ', MSDB.DFT$mzshift,'.'),
191 'mzprec', 'p', 1, 'numeric', paste0('Tolerance on m/z. Default is ', MSDB.DFT$mzprec,'.'),
192 'mztolunit', 'u', 1, 'character', paste0('Unit used for tolerance values (options -s and -p) on M/Z. Default is ', MSDB.DFT$mztolunit,'.')
193 )
194
195 if (is.null(sections) || 'rt' %in% sections)
196 spec <- c(spec,
197 'all-cols', 'A', 0, 'logical', 'Use all available chromatographic columns to match retention times.',
198 'rtcol', 'c', 1, 'character', paste0('Chromatographic column to use. Unset by default. If set, use the corresponding column to filter on retention times, if retention times are provided.'),
199 'check-cols', 'k', 0, 'logical', 'Check that the chromatographic column names specified with option -c really exist.',
200 'list-cols', 'l', 0, 'logical', 'List all chromatographic columns present in the database. Write list inside the file specified by -o option.',
201 'rttol', 'r', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
202 'rttolx', 'x', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
203 'rttoly', 'y', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
204 'rtunit', 'v', 1, 'character', paste0('Retention time unit for the input file. Default is ', MSDB.DFT$rtunit, '. Allowed values are:', paste(MSDB.RTUNIT.VALS, collapse = ", "), '.')
205 )
206
207 if (is.null(sections) || 'precursor' %in% sections)
208 spec <- c(spec,
209 'precursor-match', 'Q', 0, 'logical', 'Remove peaks whose molecule precursor peak has not been matched. Unset by default.',
210 'precursor-rt-tol', 'R', 1, 'numeric', paste0('Precursor retention time tolerance. Only used when precursor-match is enabled. Default is ', MSDB.DFT[['precursor-rt-tol']], '.'),
211 'pos-prec', 'Y', 1, 'character', paste0('Set the list of precursors to use in positive mode. Default is "', MSDB.DFT[['pos-prec']], '".'),
212 'neg-prec', 'Z', 1, 'character', paste0('Set the list of precursors to use in negative mode. Default is "', MSDB.DFT[['neg-prec']], '".')
213 )
214
215 if (is.null(sections) || 'output' %in% sections)
216 spec <- c(spec,
217 'output-file', 'o', 1, 'character', 'Set file to use for the main output.',
218 'peak-output-file', 'O', 1, 'character', 'If set and if --same-rows is set, then output all matches inside the specified file, with one mz match per line. The output columns are: mz, rt, id, col, colrt, composition, attribution. This means that if an mz value is matched several times, then it will repeated on several lines, with one match description per line.',
219 'html-output-file', 'H', 1, 'character', 'Set file to use for the HTML output.',
220 'no-main-table-in-html-output', 't', 0, 'logical', 'Do not display main table in HTML output.',
221 'same-rows', 'a', 0, 'logical', 'If set, output exactly the same number of rows as the input. This means that in case of multiple matches for one mz, then only one line is output (i.e.: the mz value is not duplicated on several lines). In the main output file, an "ms.matching" column is output with inside, for each mz, a comma separated list of matched component/molecule IDs. If unset, then only the main output file is used, and one single is written to it with one line per peak match, and eventual mz line duplicated if there are multiple matches for this mz.',
222 'same-cols', 'b', 0, 'logical', 'If set, output the same columns as inside the input. All input columns are copied to the output.',
223 'molids-sep', 'S', 1, 'character', paste0('Set character separator used to when concatenating molecule IDs in output. Default is "', MSDB.DFT[['molids-sep']] , '".'),
224 'first-val', '1', 0, 'logical', 'Keep only the first value in multi-value fields. Unset by default.',
225 'excel2011comp', 'X', 0, 'logical', 'Excel 2011 compatiblity mode. Output ASCII text files instead of UTF-8 files, where greek letters are replaced with their latin names, plusminus sign is replaced with +- and apostrophe is replaced with \"prime\". All other non-ASCII characters are repladed with underscore.'
226 )
227
228 if (is.null(sections) || 'database' %in% sections)
229 spec <- c(spec,
230 'database', 'd', 1, 'character', paste0('Set database to use: "xls" for an Excel database, "file" for a single file database, "4tabsql" for a 4Tab SQL database, and "peakforest" for a connection to PeakForest database.'),
231 'url', 'W', 1, 'character', 'URL of database. For "peakforest" database it is the HTTP URL, for the "xls" database it is the path to the directory containing the Excel files, for the "file" database it is the path to the file database and for the "4tabsql" database it is the IP address of the server.',
232 'cache-dir', 'C', 1, 'character', 'Path to directory where to store cache files. Only used when database flag is set to "xls".',
233 'db-name', 'N', 1, 'character', 'Name of the database. Used by the "4tabsql" database.',
234 'db-user', 'U', 1, 'character', 'User of the database. Used by the "4tabsql" database.',
235 'db-password', 'P', 1, 'character', 'Password of the database user. Used by the "4tabsql" database.',
236 'db-ms-modes', 'M', 1, 'character', paste0('Comma separated key/value list giving the MS modes to be used in the single file database. Default is "', MSDB.DFT[['db-ms-modes']], '".'),
237 'db-rt-unit', 'V', 1, 'character', paste0('Retention time unit for the database, used in the single file database. Default is "', MSDB.DFT[['db-rt-unit']], '". Allowed values are:', paste(MSDB.RTUNIT.VALS, collapse = ", "), '.'),
238 'db-token', 'T', 1, 'character', 'Database token. Used by Peakforest database.',
239 'db-fields', 'F', 1, 'character', paste0('Comma separated key/value list giving the field names to be used in the single file database. Default is "', MSDB.DFT[['db-fields']], '".')
240 )
241
242 if (is.null(sections) || 'misc' %in% sections)
243 spec <- c(spec,
244 'help', 'h', 0, 'logical', 'Print this help.',
245 'debug', 'g', 0, 'logical', 'Set debug mode.'
246 )
247
248 return(spec)
249 }
250
251 # Read args {{{1
252 ################################################################
253
254 read_args <- function() {
255
256 # Get options
257 opt <- getopt(matrix(make.getopt.spec(), byrow = TRUE, ncol = 5))
258
259 # help
260 if ( ! is.null(opt$help)) {
261 print.help()
262 quit()
263 }
264
265 opt <- set.dft.arg.val(opt) # Set default values
266 opt <- parse.arg.val(opt) # Parse list values
267
268 # Check values
269 error <- check.args(opt)
270
271 return(opt)
272 }
273
274 # Check args {{{1
275 ################################################################
276
277 check.args <- function(opt) {
278
279 # Check database type
280 if (is.null(opt$database))
281 stop("You must provide a database type through --database option.")
282 if ( ! opt$database %in% MSDB.VALS)
283 stop(paste0("Invalid value \"", opt$database, "\" for --database option."))
284
285 # Check filedb database
286 if (opt$database == MSDB.FILE) {
287 if (is.null(opt$url))
288 stop("When using single file database, you must specify the location of the database file with option --url.")
289 if ( ! file.exists(opt$url))
290 stop(paste0("The file path \"", opt$url,"\" specified with --db-file option is not valid."))
291 }
292
293 # Check Excel database
294 if (opt$database == MSDB.XLS) {
295 if (is.null(opt$url))
296 stop("When using Excel database, you must specify the location of the Excel files directory with option --url.")
297 if ( ! file.exists(opt$url))
298 stop(paste0("The directory path \"", opt$url,"\" specified with --xls-dir option is not valid."))
299 }
300
301 # Check 4 tab database
302 if (opt$database == MSDB.4TABSQL) {
303 if (is.null(opt$url))
304 stop("When using 4Tab SQL database, you must specify the URL of the SQL server with option --url.")
305 if (is.null(opt[['db-name']]))
306 stop("When using 4Tab SQL database, you must specify the database name through the --db-name option.")
307 if (is.null(opt[['db-user']]))
308 stop("When using 4Tab SQL database, you must specify the database user through the --db-user option.")
309 if (is.null(opt[['db-password']]))
310 stop("When using 4Tab SQL database, you must specify the database user password through the --db-password option.")
311 }
312
313 # Check Peakforest database
314 if (opt$database == MSDB.PEAKFOREST) {
315 if (is.null(opt$url))
316 stop("When using PeakForest database, you must specify the URL of the PeakForest server with option --url.")
317 }
318
319 if (is.null(opt[['list-cols']])) {
320
321 if (is.null(opt[['output-file']]))
322 stop("You must set a path for the output file.")
323
324 if (is.null(opt[['input-file']]))
325 stop("You must provide an input file.")
326
327 if (is.null(opt$mode) || ( ! opt$mode %in% MSDB.MODE.VALS))
328 stop("You must specify a mode through the --mode option.")
329
330 if (is.null(opt$mzprec))
331 stop("You must set a precision in MZ with the --mzprec option.")
332
333 if ( ( ! is.null(opt$rtcol) || ! is.null(opt[['all-cols']])) && (is.null(opt$rttolx) || is.null(opt$rttoly)))
334 stop("When chromatographic columns are set, you must provide values for --rttolx and -rttoly.")
335
336 if (is.null(opt$mztolunit) || ( ! opt$mztolunit %in% MSDB.MZTOLUNIT.VALS))
337 stop("You must specify an M/Z tolerance unit through the --mztolunit option.")
338 }
339 }
340
341 # Load database {{{1
342 ################################################################
343
344 .load.db <- function(opt) {
345
346 if (is.null(opt[['pos-prec']]) && is.null(opt[['neg-prec']])) {
347 precursors <- NULL
348 } else {
349 precursors <- list()
350 precursors[[MSDB.TAG.POS]] <- opt[['pos-prec']]
351 precursors[[MSDB.TAG.NEG]] <- opt[['neg-prec']]
352 }
353
354 db <- switch(opt$database,
355 peakforest = MsPeakForestDb$new(url = opt$url, useragent = USERAGENT, token = opt[['db-token']]),
356 xls = MsXlsDb$new(db_dir = opt$url, cache_dir = opt[['cache-dir']]),
357 '4tabsql' = Ms4TabSqlDb$new(host = extract.address(opt$url), port = extract.port(opt$url), dbname = opt[['db-name']], user = opt[['db-user']], password = opt[['db-password']]),
358 file = MsFileDb$new(file = opt$url),
359 NULL)
360 db$setPrecursors(precursors)
361 if (db$areDbFieldsSettable())
362 db$setDbFields(opt[['db-fields']])
363 if (db$areDbMsModesSettable())
364 db$setDbMsModes(opt[['db-ms-modes']])
365 db$addObservers(MsDbLogger$new())
366
367 return(db)
368 }
369
370 # Output HTML {{{1
371 ################################################################
372
373 output.html <- function(db, peaks, file) {
374
375 # Replace public database IDs by URLs
376 if ( ! is.null(peaks)) {
377 # Conversion from extdb id field to extdb name
378 extdb2classdb = list()
379 extdb2classdb[MSDB.TAG.KEGG] = BIODB.KEGG
380 extdb2classdb[MSDB.TAG.HMDB] = BIODB.HMDB
381 extdb2classdb[MSDB.TAG.CHEBI] = BIODB.CHEBI
382 extdb2classdb[MSDB.TAG.PUBCHEM] = BIODB.PUBCHEMCOMP
383
384 # Loop on all dbs
385 for (extdb in c(MSDB.TAG.KEGG, MSDB.TAG.HMDB, MSDB.TAG.CHEBI, MSDB.TAG.PUBCHEM)) {
386 if ( ! is.null(peaks) && extdb %in% colnames(peaks))
387 peaks[[extdb]] <- vapply(peaks[[extdb]], function(id) if (is.na(id)) '' else paste0('<a href="', get.entry.url(class = extdb2classdb[[extdb]], accession = id, content.type = BIODB.HTML), '">', id, '</a>'), FUN.VALUE = '')
388 }
389 }
390
391 # Write HTML
392 html <- HtmlWriter(file = file)
393 html$writeBegTag('html')
394 html$writeBegTag('header')
395 html$writeTag('meta', attr = c(charset = "UTF-8"))
396 html$writeTag('title', text = "LC/MS matching results")
397 html$writeBegTag('style')
398 html$write('table, th, td { border-collapse: collapse; }')
399 html$write('table, th { border: 1px solid black; }')
400 html$write('td { border-left: 1px solid black; border-right: 1px solid black; }')
401 html$write('th, td { padding: 5px; }')
402 html$write('th { background-color: LightBlue; }')
403 html$write('tr:nth-child(even) { background-color: LemonChiffon; }')
404 html$write('tr:nth-child(odd) { background-color: LightGreen; }')
405 html$writeEndTag('style')
406 html$writeEndTag('header')
407 html$writeBegTag('body')
408
409 # Write results
410 results <- FALSE
411 if ( ! is.null(peaks) && nrow(peaks) > 0) {
412 html$writeTag('h3', text = "Matched peaks")
413 html$writeTable(peaks)
414 results <- TRUE
415 }
416 if ( ! results)
417 html$writeTag('p', 'None.')
418
419 html$writeEndTag('body')
420 html$writeEndTag('html')
421 }
422
423 # MAIN {{{1
424 ################################################################
425
426 # Read command line arguments
427 opt <- read_args()
428
429 if (is.null(opt$debug)) {
430 options(error = function() { quit(status = 1) }, warn = 0 )
431 }
432
433 # Load database
434 source(file.path(dirname(script.path), DB.SRC.FILE[[opt$database]]), chdir = TRUE)
435 db <- .load.db(opt)
436
437 # Print columns
438 if ( ! is.null(opt[['list-cols']])) {
439 cols <- db$getChromCol()
440 df.write.tsv(cols, file = if (is.null(opt[['output-file']])) stdout() else opt[['output-file']])
441 q(status = 0)
442 }
443
444 # Read input
445 if ( ! is.null(opt[['input-file']]) && ! file.exists(opt[['input-file']]))
446 stop(paste0("Input file \"", opt[['input-file']], "\" does not exist."))
447 if (file.info(opt[['input-file']])$size > 0) {
448
449 # Load file into data frame
450 input <- read.table(file = opt[['input-file']], header = TRUE, sep = "\t", stringsAsFactor = FALSE, check.names = FALSE, comment.char = '')
451
452 # Convert each column that is identified by a number into a name
453 for (field in names(opt[['input-col-names']])) {
454 if ( ! opt[['input-col-names']][[field]] %in% colnames(input) && length(grep('^[0-9]+$', opt[['input-col-names']][[field]])) > 0) {
455 col.index <- as.integer(opt[['input-col-names']][[field]])
456 if (col.index < 1 || col.index > length(colnames(input)))
457 stop(paste0("No column n°", col.index, " for input field ", field, "."))
458 opt[['input-col-names']][[field]] <- colnames(input)[[col.index]]
459 }
460 }
461 } else {
462 input <- data.frame()
463 input[[opt[['input-col-names']][['mz']]]] <- double()
464 input[[opt[['input-col-names']][['rt']]]] <- double()
465 }
466
467 # Check mz column
468 if ( ! opt[['input-col-names']][['mz']] %in% colnames(input))
469 stop(paste0('No column named "', opt[['input-col-names']][['mz']], '" in input file.'))
470
471 # Set columns 'all-cols' specified
472 if ( ! is.null(opt[['all-cols']]))
473 opt$rtcol <- db$getChromCol()[['id']]
474
475 # Check chrom columns
476 if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) {
477 dbcols <- db$getChromCol()[['id']]
478 unknown.cols <- opt$rtcol[ ! opt$rtcol %in% dbcols]
479 if (length(unknown.cols) > 0) {
480 stop(paste0("Unknown chromatographic column", (if (length(unknown.cols) > 1) 's' else ''), ': ', paste(unknown.cols, collapse = ', '), ".\nAllowed chromatographic column names are:\n", paste(dbcols, collapse = "\n")))
481 }
482 }
483
484 # Check that an RT column exists when using MZ/RT matching
485 if ( ! is.null(opt$rtcol) && ! opt[['input-col-names']][['rt']] %in% colnames(input))
486 stop(paste0("You are running an MZ/RT match run on your input data, but no retention time column named '", opt[['input-col-names']][['rt']],"' can be found inside your input file."))
487
488 # Set output col names
489 output.col.names <- opt[['input-col-names']]
490
491 # Set streams
492 input.stream <- MsDbInputDataFrameStream$new(df = input, input.fields = opt[['input-col-names']], rtunit = opt[['rtunit']])
493 main.output <- MsDbOutputDataFrameStream$new(keep.unused = ! is.null(opt[['same-cols']]), output.fields = output.col.names, one.line = ! is.null(opt[['same-rows']]), match.sep = opt[['molids-sep']], first.val = ! is.null(opt[['first-val']]), ascii = ! is.null(opt[['excel2011comp']]), nogreek = ! is.null(opt[['excel2011comp']]), noapostrophe = ! is.null(opt[['excel2011comp']]), noplusminus = ! is.null(opt[['excel2011comp']]), rtunit = opt[['rtunit']])
494 peaks.output <- MsDbOutputDataFrameStream$new(keep.unused = ! is.null(opt[['same-cols']]), output.fields = output.col.names, first.val = ! is.null(opt[['first-val']]), ascii = ! is.null(opt[['excel2011comp']]), nogreek = ! is.null(opt[['excel2011comp']]), noapostrophe = ! is.null(opt[['excel2011comp']]), noplusminus = ! is.null(opt[['excel2011comp']]), rtunit = opt[['rtunit']])
495 invisible(db$setInputStream(input.stream))
496 db$addOutputStreams(c(main.output, peaks.output))
497
498 # Set database units
499 db$setMzTolUnit(opt$mztolunit)
500 if ( ! is.null(opt[['db-rt-unit']]) && opt$database == 'file')
501 db$setRtUnit(opt[['db-rt-unit']])
502
503 # Search database
504 mode <- if (opt$mode == POS_MODE) MSDB.TAG.POS else MSDB.TAG.NEG
505 db$searchForMzRtList(mode = mode, shift = opt$mzshift, prec = opt$mzprec, rt.tol = opt$rttol, rt.tol.x = opt$rttolx, rt.tol.y = opt$rttoly, col = opt$rtcol, precursor.match = ! is.null(opt[['precursor-match']]), precursor.rt.tol = opt[['precursor-rt-tol']])
506
507 # Write output
508 main.output$moveColumnsToBeginning(colnames(input))
509 peaks.output$moveColumnsToBeginning(colnames(input))
510 # TODO Create a class MsDbOutputCsvFileStream
511 df.write.tsv(main.output$getDataFrame(), file = opt[['output-file']], row.names = FALSE)
512 if ( ! is.null(opt[['peak-output-file']]))
513 # TODO Create a class MsDbOutputCsvFileStream
514 df.write.tsv(peaks.output$getDataFrame(), file = opt[['peak-output-file']], row.names = FALSE)
515 if ( ! is.null(opt[['html-output-file']]))
516 # TODO Create a class MsDbOutputHtmlFileStream
517 output.html(db = db, peaks = peaks.output$getDataFrame(), file = opt[['html-output-file']])