Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison frag4feature.R @ 0:7f3183988100 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author computational-metabolomics
date Wed, 27 Nov 2019 13:51:34 -0500
parents
children 18c0038dde9c
comparison
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-1:000000000000 0:7f3183988100
1 library(optparse)
2 library(msPurity)
3 library(xcms)
4 print(sessionInfo())
5
6 xset_pa_filename_fix <- function(opt, pa, xset=NULL){
7
8
9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
12
13 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
14 filepaths <- filepaths[filepaths != ""]
15 new_names <- basename(filepaths)
16
17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
18 galaxy_names <- galaxy_names[galaxy_names != ""]
19
20 nsave <- names(pa@fileList)
21 old_filenames <- basename(pa@fileList)
22
23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
24 names(pa@fileList) <- nsave
25
26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
28 }
29 print(pa@fileList)
30
31 if(!is.null(xset)){
32
33 print(xset@filepaths)
34
35 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
36 if(!all(names(pa@fileList)==basename(xset@filepaths))){
37 print('FILELISTS DO NOT MATCH')
38 message('FILELISTS DO NOT MATCH')
39 quit(status = 1)
40 }else{
41 xset@filepaths <- unname(pa@fileList)
42 }
43 }
44 }
45
46 return(list(pa, xset))
47 }
48
49
50 option_list <- list(
51 make_option(c("-o", "--out_dir"), type="character"),
52 make_option("--pa", type="character"),
53 make_option("--xset", type="character"),
54 make_option("--ppm", default=10),
55 make_option("--plim", default=0.0),
56 make_option("--convert2RawRT", action="store_true"),
57 make_option("--intense", action="store_true"),
58 make_option("--createDB", action="store_true"),
59 make_option("--cores", default=4),
60 make_option("--mzML_files", type="character"),
61 make_option("--galaxy_names", type="character"),
62 make_option("--grp_peaklist", type="character"),
63 make_option("--useGroup", action="store_true")
64 )
65
66 # store options
67 opt<- parse_args(OptionParser(option_list=option_list))
68 print(opt)
69
70 loadRData <- function(rdata_path, name){
71 #loads an RData file, and returns the named xset object if it is there
72 load(rdata_path)
73 return(get(ls()[ls() %in% name]))
74 }
75
76 # This function retrieve a xset like object
77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
78 getxcmsSetObject <- function(xobject) {
79 # XCMS 1.x
80 if (class(xobject) == "xcmsSet")
81 return (xobject)
82 # XCMS 3.x
83 if (class(xobject) == "XCMSnExp") {
84 # Get the legacy xcmsSet object
85 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
86 sampclass(xset) <- xset@phenoData$sample_group
87 return (xset)
88 }
89 }
90
91 # Requires
92 pa <- loadRData(opt$pa, 'pa')
93 xset <- loadRData(opt$xset, c('xset','xdata'))
94 xset <- getxcmsSetObject(xset)
95
96 pa@cores <- opt$cores
97
98 print(pa@fileList)
99 print(xset@filepaths)
100
101 if(is.null(opt$intense)){
102 intense = FALSE
103 }else{
104 intense = TRUE
105 }
106
107 if(is.null(opt$convert2RawRT)){
108 convert2RawRT = FALSE
109 }else{
110 convert2RawRT= TRUE
111 }
112
113 if(is.null(opt$createDB)){
114 createDB = FALSE
115 }else{
116 createDB = TRUE
117 }
118
119 if(is.null(opt$useGroup)){
120 fix <- xset_pa_filename_fix(opt, pa, xset)
121 pa <- fix[[1]]
122 xset <- fix[[2]]
123 useGroup=FALSE
124 }else{
125 # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
126 print('useGroup')
127 fix <- xset_pa_filename_fix(opt, pa)
128 pa <- fix[[1]]
129 useGroup=TRUE
130 }
131
132
133 if(is.null(opt$grp_peaklist)){
134 grp_peaklist = NA
135 }else{
136 grp_peaklist = opt$grp_peaklist
137 }
138 print(useGroup)
139
140
141
142 pa <- msPurity::frag4feature(pa=pa,
143 xset=xset,
144 ppm=opt$ppm,
145 plim=opt$plim,
146 intense=intense,
147 convert2RawRT=convert2RawRT,
148 db_name='alldata.sqlite',
149 out_dir=opt$out_dir,
150 grp_peaklist=grp_peaklist,
151 create_db=createDB,
152 use_group=useGroup)
153
154 print(pa)
155 save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData'))
156
157 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
158
159 print(head(pa@grped_df))
160 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t')