Mercurial > repos > pieterlukasse > prims_metabolomics

comparison metaMS_cmd_annotate.r @ 53:70574a6381ea

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small fixes
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 14:09:27 +0100
parents f772a5caa86a
children
comparison
equal deleted inserted replaced
52:5b1adc49700d 53:70574a6381ea
8 args.settings <- args[3] 8 args.settings <- args[3]
9 9
10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt" 10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
11 args.outAnnotationTable <- args[4] 11 args.outAnnotationTable <- args[4]
12 12
13 args.mass_error_function <- args[5]
14 if (args.mass_error_function == "0")
15 args.mass_error_function <- NULL
13 ## report files 16 ## report files
14 args.htmlReportFile <- args[5] 17 args.htmlReportFile <- args[6]
15 args.htmlReportFile.files_path <- args[6] 18 args.htmlReportFile.files_path <- args[7]
16 19
17 if (length(args) == 7) 20 if (length(args) == 8)
18 { 21 {
19 args.outLogFile <- args[7] 22 args.outLogFile <- args[8]
20 # suppress messages: 23 # suppress messages:
21 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 24 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
22 msg <- file(args.outLogFile, open="wt") 25 msg <- file(args.outLogFile, open="wt")
23 sink(msg, type="message") 26 sink(msg, type="message")
24 sink(msg, type="output") 27 sink(msg, type="output")
41 source(args.settings, local=tempEnv) 44 source(args.settings, local=tempEnv)
42 message(paste(" loaded : ", args.settings)) 45 message(paste(" loaded : ", args.settings))
43 46
44 # Just to highlight: if you want to use more than one 47 # Just to highlight: if you want to use more than one
45 # trigger runLC: 48 # trigger runLC:
46 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE) 49 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, errf=args.mass_error_function, nSlaves=20, returnXset = TRUE)
47 50
48 # write out runLC annotation results: 51 # write out runLC annotation results:
49 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE) 52 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
50 53
51 # the used constructed DB (write to log): 54 # the used constructed DB (write to log):
52 cat("\nConstructed DB info===============:\n") 55 cat("\nConstructed DB info===============:\n")
53 str(tempEnv[[testDB[1]]]$Info) 56 str(tempEnv[[testDB[1]]]$Info)
54 cat("\nConstructed DB table===============:\n") 57 cat("\nConstructed DB table===============:\n")
55 if (length(args) == 7) 58 if (length(args) == 8)
56 { 59 {
57 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE) 60 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
58 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE) 61 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
59 } 62 }
60 63