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comparison create_sqlite_db.R @ 11:86e37ad9ff31 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
author tomnl
date Mon, 07 May 2018 12:00:04 -0400
parents 26fd52ed6d21
children 291c9c7f63da
comparison
equal deleted inserted replaced
10:e9026031dab3 11:86e37ad9ff31
55 make_option("--cores", default=4), 55 make_option("--cores", default=4),
56 make_option("--mzML_files", type="character"), 56 make_option("--mzML_files", type="character"),
57 make_option("--galaxy_names", type="character"), 57 make_option("--galaxy_names", type="character"),
58 make_option("--grp_peaklist", type="character"), 58 make_option("--grp_peaklist", type="character"),
59 make_option("--db_name", type="character", default='lcms_data.sqlite'), 59 make_option("--db_name", type="character", default='lcms_data.sqlite'),
60 make_option("--raw_rt_columns", action="store_true") 60 make_option("--raw_rt_columns", action="store_true"),
61 make_option("--metfrag_result", type="character"),
62 make_option("--sirius_csifingerid_result", type="character")
61 ) 63 )
64
62 65
63 # store options 66 # store options
64 opt<- parse_args(OptionParser(option_list=option_list)) 67 opt<- parse_args(OptionParser(option_list=option_list))
65 68
66 loadRData <- function(rdata_path, name){ 69 loadRData <- function(rdata_path, name){
73 print(opt$xset) 76 print(opt$xset)
74 print(opt$xcms_camera_option) 77 print(opt$xcms_camera_option)
75 # Requires 78 # Requires
76 pa <- loadRData(opt$pa, 'pa') 79 pa <- loadRData(opt$pa, 'pa')
77 80
78 print('TESTETSTESTETE') 81
79 print(pa@fileList) 82 print(pa@fileList)
80 83
81 84
82 if (opt$xcms_camera_option=='xcms'){ 85 if (opt$xcms_camera_option=='xcms'){
83 xset <- loadRData(opt$xset, 'xset') 86 xset <- loadRData(opt$xset, 'xset')
124 px <- msPurity::purityX(xset, saveEIC = TRUE, 127 px <- msPurity::purityX(xset, saveEIC = TRUE,
125 cores=opt$cores, sqlitePth=db_pth, 128 cores=opt$cores, sqlitePth=db_pth,
126 rtrawColumns = rtrawColumns) 129 rtrawColumns = rtrawColumns)
127 } 130 }
128 131
132 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
133
134 add_extra_table <- function(name, pth){
135
136 print('CHECK1')
137 print(name)
138 print(pth)
139 if (!is.null(pth)){
140 print('CHECK2')
141 print(pth)
142 df <- read.table(pth, header = TRUE, sep='\t', stringsAsFactors = FALSE, comment.char = "")
143 # bug for repeating headers
144 df <- df[!df$UID=='UID',]
145
146 # get peakid, an scan id
147 df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
148 colnames(df_ids) <- c('grp_id', 'file_id', 'peak_id')
149 df <- cbind(df_ids, df)
150 # export to database
151
152
153 DBI::dbWriteTable(con, name=name, value=df, row.names=FALSE)
154
155 }
156
157 }
158
159 add_extra_table('metfrag_results', opt$metfrag_result)
160 add_extra_table('sirius_csifingerid_results', opt$sirius_csifingerid_result)
129 161
130 162
131 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
132 163
133 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ', 164 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
134 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ', 165 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
135 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ', 166 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
136 'FROM c_peak_groups AS cpg ', 167 'FROM c_peak_groups AS cpg ',