Mercurial > repos > pieterlukasse > prims_metabolomics

annotate metaMS_cmd_annotate.r @ 49:f772a5caa86a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents
children 70574a6381ea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
1 ## read args:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
2 args <- commandArgs(TRUE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
3 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
4 args.constructedDB <- args[1]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
5 ## data file in xset format:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
6 args.xsetData <- args[2]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
7 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
8 args.settings <- args[3]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
9
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
11 args.outAnnotationTable <- args[4]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
12
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
13 ## report files
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
14 args.htmlReportFile <- args[5]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
15 args.htmlReportFile.files_path <- args[6]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
16
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
17 if (length(args) == 7)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
18 {
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
19 args.outLogFile <- args[7]
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
20 # suppress messages:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
21 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
22 msg <- file(args.outLogFile, open="wt")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
23 sink(msg, type="message")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
24 sink(msg, type="output")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
25 }
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
26
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
27 cat("\nSettings used===============:\n")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
28 cat(readChar(args.settings, 1e5))
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
29
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
30
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
31 tryCatch(
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
32 {
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
33 library(metaMS)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
34
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
35 ## load the constructed DB :
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
36 tempEnv <- new.env()
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
37 testDB <- load(args.constructedDB, envir=tempEnv)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
38 xsetData <- readRDS(args.xsetData)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
39
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
40 ## load settings "script" into "customMetaMSsettings"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
41 source(args.settings, local=tempEnv)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
42 message(paste(" loaded : ", args.settings))
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
43
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
44 # Just to highlight: if you want to use more than one
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
45 # trigger runLC:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
46 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
47
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
48 # write out runLC annotation results:
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
49 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
50
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
51 # the used constructed DB (write to log):
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
52 cat("\nConstructed DB info===============:\n")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
53 str(tempEnv[[testDB[1]]]$Info)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
54 cat("\nConstructed DB table===============:\n")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
55 if (length(args) == 7)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
56 {
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
57 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
58 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
59 }
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
60
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
61 message("\nGenerating report.........")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
62 # report
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
63 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
64 html <- "<html><body><h1>Summary of annotation results:</h1>"
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
65 nrTotalFeatures <- nrow(LC$PeakTable)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
66 nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
67 html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
68 html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
69
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
70 html <- paste(html,"</body><html>")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
71 message("finished generating report")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
72 write(html,file=args.htmlReportFile)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
73 # unlink(args.htmlReportFile)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
74 cat("\nWarnings================:\n")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
75 str( warnings() )
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
76 },
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
77 error=function(cond) {
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
78 sink(NULL, type="message") # default setting
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
79 sink(stderr(), type="output")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
80 message("\nERROR: ===========\n")
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
81 print(cond)
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
82 }
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
diff changeset
83 )