--- a/spectral_matching.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-library(msPurity)
-library(msPurityData)
-library(optparse)
-print(sessionInfo())
-
-
-option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--target_db_pth", type="character"),
-  make_option("--library_db_pth", type="character", default=NA),
-  make_option("--ra_thres_l", default=0),
-  make_option("--ra_thres_t", default=2),
-  make_option("--cores", default=1),
-  make_option("--pol", default='positive'),
-  make_option("--ppm_tol_prod", default=10),
-  make_option("--ppm_tol_prec", default=5),
-  make_option("--score_thres", default=0.6),
-  make_option("--instrument_types", type='character'),
-  make_option("--library_sources", type='character'),
-  make_option("--scan_ids", default=NA),
-  make_option("--topn", default=NA),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--create_new_database", action="store_true")
-
-)
-
-# store options
-opt<- parse_args(OptionParser(option_list=option_list))
-
-
-
-if (!is.null(opt$create_new_database)){
-    target_db_pth <-  file.path(opt$out_dir, 'db_with_spectral_matching.sqlite')
-    file.copy(opt$target_db_pth, target_db_pth)
-}else{
-    target_db_pth <- opt$target_db_pth
-}
-
-
-if (opt$instrument_types=='None'){
-    instrument_types <- NA
-}else{
-    instrument_types <- trimws(strsplit(opt$instrument_types, ',')[[1]])
-}
-if (opt$library_sources=='None'){
-    library_sources <- NA
-}else{
-    library_sources <- trimws(strsplit(opt$library_sources, ',')[[1]])
-}
-
-
-if (!is.na(opt$scan_ids)){
-    scan_ids <- trimws(strsplit(opt$scan_ids, ',')[[1]])
-    scan_ids <- scan_ids[scan_ids != ""]
-}else{
-    scan_ids <- NA
-}
-
-
-print(instrument_types)
-print(library_sources)
-print(scan_ids)
-
-result <- msPurity::spectral_matching(
-                            target_db_pth =target_db_pth ,
-                            library_db_pth = opt$library_db_pth,
-                            ra_thres_l = opt$ra_thres_l,
-                            ra_thres_t = opt$ra_thres_t,
-                            cores = opt$cores,
-                            pol = opt$pol,
-                            ppm_tol_prod = opt$ppm_tol_prod,
-                            ppm_tol_prec = opt$ppm_tol_prec,
-                            score_thres = opt$score_thres,
-                            out_dir = opt$out_dir,
-                            topn = opt$topn,
-                            grp_peaklist = NA,
-
-                            instrument_types = instrument_types,
-                            library_sources = library_sources,
-                            scan_ids = scan_ids)
-
-print(file.path(result$result_db_pth))
-
-write.table(result$xcms_summary_df, file.path(opt$out_dir, 'xcms_hits.tsv'), row.names=FALSE, sep='\t')
-
-con <- DBI::dbConnect(RSQLite::SQLite(), file.path(result$result_db_pth))
-# con <- DBI::dbConnect(RSQLite::SQLite(), file.path(opt$out_dir, 'result.sqlite'))
-
-cmd <- paste('SELECT * FROM matches
-              LEFT JOIN library_meta ON matches.lid=library_meta.lid
-              LEFT JOIN s_peak_meta ON matches.pid=s_peak_meta.pid
-              LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid
-              WHERE matches.score >= ', opt$score_thres)
-print(cmd)
-scan_hits <- DBI::dbGetQuery(con, cmd)
-
-write.table(scan_hits, file.path(opt$out_dir, 'scan_hits.tsv'), row.names=FALSE, sep='\t')