Mercurial > repos > tomnl > flag_remove_peaks

annotate spectral_matching.R @ 14:088f318b2944 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 05:57:15 -0400
parents cb8dce9812ff
children
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1 library(msPurity)
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2 library(msPurityData)
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3 library(optparse)
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4 print(sessionInfo())
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7 option_list <- list(
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8 make_option(c("-o", "--out_dir"), type="character"),
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9 make_option("--target_db_pth", type="character"),
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10 make_option("--library_db_pth", type="character", default=NA),
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11 make_option("--ra_thres_l", default=0),
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12 make_option("--ra_thres_t", default=2),
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13 make_option("--cores", default=1),
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14 make_option("--pol", default='positive'),
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15 make_option("--ppm_tol_prod", default=10),
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16 make_option("--ppm_tol_prec", default=5),
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17 make_option("--score_thres", default=0.6),
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18 make_option("--instrument_types", type='character'),
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19 make_option("--library_sources", type='character'),
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20 make_option("--scan_ids", default=NA),
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21 make_option("--topn", default=NA),
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22 make_option("--mzML_files", type="character"),
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23 make_option("--galaxy_names", type="character"),
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24 make_option("--create_new_database", action="store_true")
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26 )
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28 # store options
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29 opt<- parse_args(OptionParser(option_list=option_list))
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33 if (!is.null(opt$create_new_database)){
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34 target_db_pth <- file.path(opt$out_dir, 'db_with_spectral_matching.sqlite')
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35 file.copy(opt$target_db_pth, target_db_pth)
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36 }else{
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37 target_db_pth <- opt$target_db_pth
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38 }
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40
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41 if (opt$instrument_types=='None'){
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42 instrument_types <- NA
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43 }else{
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44 instrument_types <- trimws(strsplit(opt$instrument_types, ',')[[1]])
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45 }
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46 if (opt$library_sources=='None'){
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47 library_sources <- NA
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48 }else{
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49 library_sources <- trimws(strsplit(opt$library_sources, ',')[[1]])
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50 }
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53 if (!is.na(opt$scan_ids)){
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54 scan_ids <- trimws(strsplit(opt$scan_ids, ',')[[1]])
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55 scan_ids <- scan_ids[scan_ids != ""]
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56 }else{
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57 scan_ids <- NA
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58 }
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59
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60
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61 print(instrument_types)
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62 print(library_sources)
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63 print(scan_ids)
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64
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65 result <- msPurity::spectral_matching(
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66 target_db_pth =target_db_pth ,
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67 library_db_pth = opt$library_db_pth,
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68 ra_thres_l = opt$ra_thres_l,
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69 ra_thres_t = opt$ra_thres_t,
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70 cores = opt$cores,
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71 pol = opt$pol,
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72 ppm_tol_prod = opt$ppm_tol_prod,
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73 ppm_tol_prec = opt$ppm_tol_prec,
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74 score_thres = opt$score_thres,
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75 out_dir = opt$out_dir,
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76 topn = opt$topn,
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77 grp_peaklist = NA,
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78
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79 instrument_types = instrument_types,
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80 library_sources = library_sources,
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81 scan_ids = scan_ids)
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82
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83 print(file.path(result$result_db_pth))
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84
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85 write.table(result$xcms_summary_df, file.path(opt$out_dir, 'xcms_hits.tsv'), row.names=FALSE, sep='\t')
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86
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87 con <- DBI::dbConnect(RSQLite::SQLite(), file.path(result$result_db_pth))
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88 # con <- DBI::dbConnect(RSQLite::SQLite(), file.path(opt$out_dir, 'result.sqlite'))
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89
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90 cmd <- paste('SELECT * FROM matches
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91 LEFT JOIN library_meta ON matches.lid=library_meta.lid
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92 LEFT JOIN s_peak_meta ON matches.pid=s_peak_meta.pid
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93 LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid
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94 WHERE matches.score >= ', opt$score_thres)
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95 print(cmd)
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96 scan_hits <- DBI::dbGetQuery(con, cmd)
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97
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98 write.table(scan_hits, file.path(opt$out_dir, 'scan_hits.tsv'), row.names=FALSE, sep='\t')