Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

comparison frag4feature.R @ 6:cc0f8ddad4a8 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:28:18 +0000
parents 96af79da0cc6
children
comparison
equal deleted inserted replaced
5:31920dd28862 6:cc0f8ddad4a8
1 library(optparse) 1 library(optparse)
2 library(msPurity) 2 library(msPurity)
3 library(xcms) 3 library(xcms)
4 print(sessionInfo()) 4 print(sessionInfo())
5 5
6 xset_pa_filename_fix <- function(opt, pa, xset=NULL){ 6 xset_pa_filename_fix <- function(opt, pa, xset=NULL) {
7 7
8 8
9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){ 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 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 11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
12 12
13 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) 13 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
14
14 filepaths <- filepaths[filepaths != ""] 15 filepaths <- filepaths[filepaths != ""]
15 new_names <- basename(filepaths)
16 16
17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) 17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
18 galaxy_names <- galaxy_names[galaxy_names != ""] 18 galaxy_names <- galaxy_names[galaxy_names != ""]
19 19
20 nsave <- names(pa@fileList) 20 nsave <- names(pa@fileList)
21 old_filenames <- basename(pa@fileList) 21 old_filenames <- basename(pa@fileList)
22 22
26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) 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)]) 27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
28 } 28 }
29 print(pa@fileList) 29 print(pa@fileList)
30 30
31 if(!is.null(xset)){ 31 if (!is.null(xset)) {
32 32
33 print(xset@filepaths) 33 print(xset@filepaths)
34 34
35 if(!all(basename(pa@fileList)==basename(xset@filepaths))){ 35 if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
36 if(!all(names(pa@fileList)==basename(xset@filepaths))){ 36 if (!all(names(pa@fileList) == basename(xset@filepaths))) {
37 print('FILELISTS DO NOT MATCH') 37 print("FILELISTS DO NOT MATCH")
38 message('FILELISTS DO NOT MATCH') 38 message("FILELISTS DO NOT MATCH")
39 quit(status = 1) 39 quit(status = 1)
40 }else{ 40 }else{
41 xset@filepaths <- unname(pa@fileList) 41 xset@filepaths <- unname(pa@fileList)
42 } 42 }
43 } 43 }
46 return(list(pa, xset)) 46 return(list(pa, xset))
47 } 47 }
48 48
49 49
50 option_list <- list( 50 option_list <- list(
51 make_option(c("-o", "--out_dir"), type="character"), 51 make_option(c("-o", "--out_dir"), type = "character"),
52 make_option("--pa", type="character"), 52 make_option("--pa", type = "character"),
53 make_option("--xset", type="character"), 53 make_option("--xset", type = "character"),
54 make_option("--ppm", default=10), 54 make_option("--ppm", default = 10),
55 make_option("--plim", default=0.0), 55 make_option("--plim", default = 0.0),
56 make_option("--convert2RawRT", action="store_true"), 56 make_option("--convert2RawRT", action = "store_true"),
57 make_option("--intense", action="store_true"), 57 make_option("--intense", action = "store_true"),
58 make_option("--createDB", action="store_true"), 58 make_option("--createDB", action = "store_true"),
59 make_option("--cores", default=4), 59 make_option("--cores", default = 4),
60 make_option("--mzML_files", type="character"), 60 make_option("--mzML_files", type = "character"),
61 make_option("--galaxy_names", type="character"), 61 make_option("--galaxy_names", type = "character"),
62 make_option("--grp_peaklist", type="character"), 62 make_option("--grp_peaklist", type = "character"),
63 make_option("--useGroup", action="store_true") 63 make_option("--useGroup", action = "store_true")
64 ) 64 )
65 65
66 # store options 66 # store options
67 opt<- parse_args(OptionParser(option_list=option_list)) 67 opt <- parse_args(OptionParser(option_list = option_list))
68 print(opt) 68 print(opt)
69 69
70 loadRData <- function(rdata_path, name){ 70 loadRData <- function(rdata_path, name) {
71 #loads an RData file, and returns the named xset object if it is there 71 #loads an RData file, and returns the named xset object if it is there
72 load(rdata_path) 72 load(rdata_path)
73 return(get(ls()[ls() %in% name])) 73 return(get(ls()[ls() %in% name]))
74 } 74 }
75 75
76 # This function retrieve a xset like object 76 # This function retrieve a xset like object
77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr 77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
78 getxcmsSetObject <- function(xobject) { 78 getxcmsSetObject <- function(xobject) {
79 # XCMS 1.x 79 # XCMS 1.x
80 if (class(xobject) == "xcmsSet") 80 if (class(xobject) == "xcmsSet")
81 return (xobject) 81 return(xobject)
82 # XCMS 3.x 82 # XCMS 3.x
83 if (class(xobject) == "XCMSnExp") { 83 if (class(xobject) == "XCMSnExp") {
84 # Get the legacy xcmsSet object 84 # Get the legacy xcmsSet object
85 suppressWarnings(xset <- as(xobject, 'xcmsSet')) 85 suppressWarnings(xset <- as(xobject, "xcmsSet"))
86 sampclass(xset) <- xset@phenoData$sample_group 86 sampclass(xset) <- xset@phenoData$sample_group
87 return (xset) 87 return(xset)
88 } 88 }
89 } 89 }
90 90
91 # Requires 91 # Requires
92 pa <- loadRData(opt$pa, 'pa') 92 pa <- loadRData(opt$pa, "pa")
93 xset <- loadRData(opt$xset, c('xset','xdata')) 93 xset <- loadRData(opt$xset, c("xset", "xdata"))
94 xset <- getxcmsSetObject(xset) 94 xset <- getxcmsSetObject(xset)
95 95
96 pa@cores <- opt$cores 96 pa@cores <- opt$cores
97 97
98 print(pa@fileList) 98 print(pa@fileList)
99 print(xset@filepaths) 99 print(xset@filepaths)
100 100
101 if(is.null(opt$intense)){ 101 if (is.null(opt$intense)) {
102 intense = FALSE 102 intense <- FALSE
103 }else{ 103 }else{
104 intense = TRUE 104 intense <- TRUE
105 } 105 }
106 106
107 if(is.null(opt$convert2RawRT)){ 107 if (is.null(opt$convert2RawRT)) {
108 convert2RawRT = FALSE 108 convert2RawRT <- FALSE
109 }else{ 109 }else{
110 convert2RawRT= TRUE 110 convert2RawRT <- TRUE
111 } 111 }
112 112
113 if(is.null(opt$createDB)){ 113 if (is.null(opt$createDB)) {
114 createDB = FALSE 114 createDB <- FALSE
115 }else{ 115 }else{
116 createDB = TRUE 116 createDB <- TRUE
117 } 117 }
118 118
119 if(is.null(opt$useGroup)){ 119 if (is.null(opt$useGroup)) {
120 fix <- xset_pa_filename_fix(opt, pa, xset) 120 fix <- xset_pa_filename_fix(opt, pa, xset)
121 pa <- fix[[1]] 121 pa <- fix[[1]]
122 xset <- fix[[2]] 122 xset <- fix[[2]]
123 useGroup=FALSE 123 useGroup <- FALSE
124 }else{ 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 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') 126 print("useGroup")
127 fix <- xset_pa_filename_fix(opt, pa) 127 fix <- xset_pa_filename_fix(opt, pa)
128 pa <- fix[[1]] 128 pa <- fix[[1]]
129 useGroup=TRUE 129 useGroup <- TRUE
130 } 130 }
131 131
132 132
133 if(is.null(opt$grp_peaklist)){ 133 if (is.null(opt$grp_peaklist)) {
134 grp_peaklist = NA 134 grp_peaklist <- NA
135 }else{ 135 }else{
136 grp_peaklist = opt$grp_peaklist 136 grp_peaklist <- opt$grp_peaklist
137 } 137 }
138 print(useGroup) 138 print(useGroup)
139 139
140 140 pa <- msPurity::frag4feature(pa = pa,
141 141 xset = xset,
142 pa <- msPurity::frag4feature(pa=pa, 142 ppm = opt$ppm,
143 xset=xset, 143 plim = opt$plim,
144 ppm=opt$ppm, 144 intense = intense,
145 plim=opt$plim, 145 convert2RawRT = convert2RawRT,
146 intense=intense, 146 db_name = "alldata.sqlite",
147 convert2RawRT=convert2RawRT, 147 out_dir = opt$out_dir,
148 db_name='alldata.sqlite', 148 grp_peaklist = grp_peaklist,
149 out_dir=opt$out_dir, 149 create_db = createDB,
150 grp_peaklist=grp_peaklist, 150 use_group = useGroup)
151 create_db=createDB,
152 use_group=useGroup)
153
154 print(pa) 151 print(pa)
155 save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData')) 152 save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData"))
156 153
157 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) 154 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
158 155
159 print(head(pa@grped_df)) 156 print(head(pa@grped_df))
160 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t') 157 write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")