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Commit message:
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f |
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modified:
README.rst flagRemove.R frag4feature.R macros.xml purityX.R test-data/averageFragSpectra_output_all.RData test-data/averageFragSpectra_output_all_only.RData test-data/averageFragSpectra_output_inter.RData test-data/averageFragSpectra_output_intra.RData test-data/combineAnnotations_combined_annotations.sqlite test-data/createDatabase_output.sqlite test-data/createDatabase_output_eic.sqlite test-data/createMSP_output_av_all_metadata.msp test-data/createMSP_output_av_all_metadata_custom_adducts.msp test-data/filterFragSpectra_output.RData test-data/filterFragSpectra_output_prec.tsv test-data/flagRemove_output.tsv test-data/frag4feature_output.RData test-data/frag4feature_output.tsv test-data/purityA_output.RData test-data/purityX_output.RData test-data/spectralMatching_db_with_spectral_matching.sqlite test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite |
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| diff -r a46824d13914 -r a8842e5e75a7 README.rst --- a/README.rst Wed Jun 12 16:09:13 2024 +0000 +++ b/README.rst Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -3,13 +3,13 @@ |Git| |Bioconda| |License| -Version v1.16.2+galaxy2 +Version v1.28.0+galaxy0 ------------------------ - msPurity - - bioconductor-mspurity v1.16.2 + - bioconductor-mspurity v1.28.0 - Galaxy tools - - v2 + - v0 About ------ @@ -26,10 +26,8 @@ * Bioconductor: http://bioconductor.org/packages/msPurity/ * Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html * Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf -* Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity * Github code: https://github.com/computational-metabolomics/mspurity * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity -* Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity Dependencies @@ -54,6 +52,12 @@ Changes ------------------------- +v1.28.0-galaxy0 + - Version bump to v1.28.0 + - createMSP now uses the median precursor MZ and precursor RT in the MSP files + - flagRemove updated to handle different xcms version objects internally within msPurity R function + - Relevant unit tests updated and further tidying up of repo + v1.16.2-galaxy2 - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) - Cleanup of xml based on updated lint requirements |
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| diff -r a46824d13914 -r a8842e5e75a7 flagRemove.R --- a/flagRemove.R Wed Jun 12 16:09:13 2024 +0000 +++ b/flagRemove.R Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -1,4 +1,5 @@ library(msPurity) +library(xcms) library(optparse) print(sessionInfo()) option_list <- list( @@ -117,19 +118,25 @@ print(opt) -getxcmsSetObject <- function(xobject) { - # XCMS 1.x - if (class(xobject) == "xcmsSet") { - return(xobject) - } - # XCMS 3.x - if (class(xobject) == "XCMSnExp") { - # Get the legacy xcmsSet object - suppressWarnings(xset <- as(xobject, "xcmsSet")) - xcms::sampclass(xset) <- xset@phenoData$sample_group - return(xset) - } -} +# This R function can handle both XCMS object versions (so following code +# no longer required - kept here for reference) +# getxcmsSetObject <- function(xobject) { +# # XCMS 1.x +# if (class(xobject) == "xcmsSet"){ +# return(xobject) +# } +# # XCMS 3.x +# if (class(xobject) == "XCMSnExp") { +# # Get the legacy xcmsSet object +# suppressWarnings(xset <- as(xobject, "xcmsSet")) +# if (!is.null(xset@phenoData$sample_group)){ +# xcms::sampclass(xset) <- xset@phenoData$sample_group +# }else{ +# xcms::sampclass(xset) <- "." +# } +# return(xset) +# } +# } loadRData <- function(rdata_path, name) { @@ -138,9 +145,9 @@ return(get(ls()[ls() %in% name])) } -xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata"))) +xset <- loadRData(opt$xset_path, c("xset", "xdata")) -print(xset) + if (is.null(opt$samplelist)) { blank_class <- opt$blank_class } else { @@ -157,6 +164,8 @@ } + + if (is.null(opt$multilist)) { ffrm_out <- flag_remove(xset, pol = opt$polarity, @@ -201,15 +210,6 @@ ) } else { # nolint start - # TODO - # xsets <- split(xset, multilist_df$multlist) - # - # mult_grps <- unique(multilist_df$multlist) - # - # for (mgrp in mult_grps){ - # xset_i <- xsets[mgrp] - # xcms::group(xset_i, - # - # } + # TODO - potential for multilist analysis (e) # nolint end } |
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| diff -r a46824d13914 -r a8842e5e75a7 frag4feature.R --- a/frag4feature.R Wed Jun 12 16:09:13 2024 +0000 +++ b/frag4feature.R Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -81,7 +81,11 @@ if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, "xcmsSet")) - sampclass(xset) <- xset@phenoData$sample_group + if (!is.null(xset@phenoData$sample_group)) { + xcms::sampclass(xset) <- xset@phenoData$sample_group + } else { + xcms::sampclass(xset) <- "." + } return(xset) } } @@ -96,6 +100,7 @@ print(pa@fileList) print(xset@filepaths) + if (is.null(opt$intense)) { intense <- FALSE } else { |
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| diff -r a46824d13914 -r a8842e5e75a7 macros.xml --- a/macros.xml Wed Jun 12 16:09:13 2024 +0000 +++ b/macros.xml Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -1,17 +1,17 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.16.2</token> - <token name="@GALAXY_TOOL_VERSION@">2</token> + <token name="@TOOL_VERSION@">1.28.0</token> + <token name="@GALAXY_TOOL_VERSION@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> - <requirement type="package" version="1.46.0" >bioconductor-camera</requirement> - <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement> - <requirement type="package" version="1.18.0" >bioconductor-mspuritydata</requirement> - <requirement type="package" version="1.6.6">r-optparse</requirement> - <requirement type="package" version="1.3.1">r-rpostgres</requirement> - <requirement type="package" version="0.10.21">r-rmysql</requirement> + <requirement type="package" version="1.58.0" >bioconductor-camera</requirement> + <requirement type="package" version="4.0.0" >bioconductor-xcms</requirement> + <requirement type="package" version="1.30.0" >bioconductor-mspuritydata</requirement> + <requirement type="package" version="1.7.5">r-optparse</requirement> + <requirement type="package" version="1.4.7">r-rpostgres</requirement> + <requirement type="package" version="0.10.27">r-rmysql</requirement> <yield /> </requirements> </xml> |
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| diff -r a46824d13914 -r a8842e5e75a7 purityX.R --- a/purityX.R Wed Jun 12 16:09:13 2024 +0000 +++ b/purityX.R Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -74,14 +74,18 @@ getxcmsSetObject <- function(xobject) { # XCMS 1.x - if (class(xobject) == "xcmsSet") { + if (class(xobject) == "xcmsSet"){ return(xobject) } # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, "xcmsSet")) - sampclass(xset) <- xset@phenoData$sample_group + if (!is.null(xset@phenoData$sample_group)){ + xcms::sampclass(xset) <- xset@phenoData$sample_group + }else{ + xcms::sampclass(xset) <- "." + } return(xset) } } |
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| diff -r a46824d13914 -r a8842e5e75a7 test-data/createMSP_output_av_all_metadata.msp --- a/test-data/createMSP_output_av_all_metadata.msp Wed Jun 12 16:09:13 2024 +0000 +++ b/test-data/createMSP_output_av_all_metadata.msp Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -1,6 +1,6 @@ -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+NH4]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -10,15 +10,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+H+NH3]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -28,7 +28,7 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 |
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| diff -r a46824d13914 -r a8842e5e75a7 test-data/createMSP_output_av_all_metadata_custom_adducts.msp --- a/test-data/createMSP_output_av_all_metadata_custom_adducts.msp Wed Jun 12 16:09:13 2024 +0000 +++ b/test-data/createMSP_output_av_all_metadata_custom_adducts.msp Thu Jun 13 11:43:16 2024 +0000 |
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| @@ -1,6 +1,6 @@ -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+NH4]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -10,15 +10,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+H+NH3]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -28,15 +28,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -46,15 +46,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M-H]- -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M-H]- +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -64,15 +64,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+TEST -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+TEST +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE [M+TEST AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -82,15 +82,15 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 126.53768157959 2499.31469726562 0.5 -RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:SPACE+]+ -MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 -AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:SPACE+]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532 isotope [4][M]+ MS$FOCUSED_ION: PRECURSOR_TYPE SPACE+]+ AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo @@ -100,7 +100,7 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 |
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| diff -r a46824d13914 -r a8842e5e75a7 test-data/filterFragSpectra_output_prec.tsv --- a/test-data/filterFragSpectra_output_prec.tsv Wed Jun 12 16:09:13 2024 +0000 +++ b/test-data/filterFragSpectra_output_prec.tsv Thu Jun 13 11:43:16 2024 +0000 |
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| b'@@ -1,324 +1,324 @@\n-"grpid"\t"mz"\t"mzmin"\t"mzmax"\t"rt"\t"rtmin"\t"rtmax"\t"into"\t"intf"\t"maxo"\t"maxf"\t"i"\t"sn"\t"sample"\t"cid"\t"filename"\t"inPurity"\t"pid"\t"precurMtchID"\t"precurMtchScan"\t"precurMtchRT"\t"precurMtchMZ"\t"precurMtchPPM"\t"retentionTime"\t"fileid"\t"seqNum"\t"purity_pass_flag"\n-"12"\t112.050766766484\t112.050651550293\t112.087196350098\t67.47903\t55.2769038\t80.361672\t36223791.266206\t133522503.549415\t7158012.5\t8555976.39592391\t1\t21.054952458659\t1\t9\t"LCMSMS_2.mzML"\t1\t384\t466\t462\t64.427298\t112.050704956055\t0.55162878935702\t64.958766\t1\t466\tTRUE\n-"12"\t112.05085569128\t112.050621032715\t112.120460510254\t67.634034\t55.4140188\t80.555406\t36139265.8017591\t133395720.51942\t7426335.5\t8522973.08164079\t1\t20.3803986860233\t2\t400\t"LCMSMS_1.mzML"\t1\t1218\t472\t468\t65.376156\t112.050743103027\t1.00479600749392\t65.928894\t2\t472\tTRUE\n-"14"\t113.03541992282\t113.034698486328\t113.059997558594\t83.441172\t72.006432\t95.851296\t88462324.9597518\t348004137.88132\t18599380\t22772249.3980656\t1\t27.431622141047\t1\t11\t"LCMSMS_2.mzML"\t1\t499\t604\t600\t81.93093\t113.034736633301\t6.04491512630164\t82.463394\t1\t604\tTRUE\n-"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t1\t1321\t596\t594\t81.344292\t113.034736633301\t5.61834418239318\t81.70764\t2\t596\tTRUE\n-"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t0.472133563046185\t1380\t667\t666\t90.601068\t113.034713745117\t5.8208310964319\t90.871572\t2\t667\tFALSE\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t0.950632241095866\t226\t277\t276\t40.9547952\t116.070838928223\t1.7359353575902\t41.2252842\t1\t277\tTRUE\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t281\t343\t342\t49.182402\t116.070831298828\t1.67020474130592\t49.452918\t1\t343\tTRUE\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t337\t410\t408\t57.5697876\t116.070770263672\t1.14435981103166\t57.9341562\t1\t410\tTRUE\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t0.989376188689562\t1055\t277\t276\t41.0984136\t116.070816040039\t2.22463819204545\t41.3688786\t2\t277\tTRUE\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1110\t343\t342\t49.3156656\t116.070823669434\t2.29036885341395\t49.586265\t2\t343\tTRUE\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1165\t409\t408\t57.7060356\t116.070785522461\t1.96171554657148\t57.976677\t2\t409\tTRUE\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t391\t475\t474\t65.949288\t132.101821899414\t0.0447061558976329\t66.21981\t1\t475\tTRUE\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t446\t541\t540\t74.297424\t132.101867675781\t0.301817188616646\t74.567904\t1\t541\tTRUE\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t501\t607\t606\t'..b'4711.0742877\t195241268.75592\t14374106\t12850193.8354307\t1\t21.2071228333724\t1\t"LCMSMS_2.mzML"\t371\t1\t465\t563\t558\t76.520544\t461.209899902344\t6.04192381657049\t77.141778\t1\t563\tTRUE\n+"757"\t461.20738152051\t461.121826171875\t461.243560791016\t77.474424\t65.376156\t89.831544\t48607882.314214\t192672537.990574\t14159047\t12716867.2850009\t1\t20.5600686941203\t2\t"LCMSMS_1.mzML"\t761\t1\t1299\t569\t564\t77.474424\t461.209899902344\t5.460410945608\t78.102018\t2\t569\tTRUE\n+"759"\t462.22122959389\t462.213439941406\t462.291839599609\t57.7060356\t44.7995376\t75.972048\t38559454.0832874\t105979165.236253\t3445839.75\t5926579.6352243\t1\t10.2307809194678\t2\t"LCMSMS_1.mzML"\t762\t0.944176192726551\t1187\t435\t432\t60.766158\t462.218811035156\t5.23247003559527\t61.226112\t2\t435\tTRUE\n+"787"\t476.190702761819\t476.186126708984\t476.307098388672\t81.162672\t69.717042\t92.725812\t39151803.0473944\t118893746.090445\t7816689\t8198001.40019319\t1\t14.9845576620757\t1\t"LCMSMS_2.mzML"\t378\t0.977294138555063\t474\t574\t570\t78.035046\t476.186828613281\t8.13570805892727\t78.58677\t1\t574\tTRUE\n+"787"\t476.190794182677\t476.186218261719\t476.307495117188\t81.344292\t69.864534\t92.927058\t43745001.5410773\t135433069.148731\t8875996\t9304027.49811656\t1\t15.612354791168\t2\t"LCMSMS_1.mzML"\t768\t0.917917041077806\t1303\t574\t570\t78.227304\t476.186981201172\t8.00725581423595\t78.779022\t2\t574\tTRUE\n+"787"\t476.190794182677\t476.186218261719\t476.307495117188\t81.344292\t69.864534\t92.927058\t43745001.5410773\t135433069.148731\t8875996\t9304027.49811656\t1\t15.612354791168\t2\t"LCMSMS_1.mzML"\t768\t0.990314571321696\t1309\t581\t576\t78.998916\t476.187042236328\t7.87908207170328\t79.648392\t2\t581\tTRUE\n+"812"\t487.181176540989\t487.099060058594\t487.239410400391\t66.710418\t54.5086626\t79.585674\t58453273.9503532\t230378509.09492\t15813294\t14998690.3403142\t1\t19.4416133244468\t1\t"LCMSMS_2.mzML"\t384\t1\t394\t478\t474\t65.949288\t487.177612304688\t7.31603861859596\t66.493134\t1\t478\tTRUE\n+"812"\t487.180877999963\t487.099700927734\t487.239501953125\t66.865908\t54.6427758\t78.998916\t60132074.4709007\t238189012.918308\t18110170\t15528706.5784369\t1\t19.1064097764383\t2\t"LCMSMS_1.mzML"\t774\t1\t1224\t479\t474\t66.147648\t487.177856445312\t6.20212078776047\t66.74139\t2\t479\tTRUE\n+"830"\t494.196757645669\t494.119018554688\t494.198516845703\t49.9356528\t37.8964158\t62.153292\t31096636.998985\t121560345.75829\t6061495.5\t8000920.55155143\t1\t19.2246142395834\t1\t"LCMSMS_2.mzML"\t387\t1\t280\t341\t336\t48.4095336\t494.197631835938\t1.76891138083971\t49.060251\t1\t341\tTRUE\n+"830"\t494.1970608933\t494.119293212891\t494.197875976562\t50.0837946\t38.0417766\t62.309778\t31975460.900009\t125089224.818786\t5749075.5\t8239138.02501223\t1\t18.9671855740286\t2\t"LCMSMS_1.mzML"\t776\t1\t1112\t345\t342\t49.3156656\t494.197631835938\t1.15529347093956\t49.7757558\t2\t345\tTRUE\n+"840"\t498.169308539313\t498.16845703125\t498.28955078125\t81.162672\t68.984166\t93.504684\t46040504.6258466\t180736904.384221\t9105023\t11919892.2978446\t1\t18.9934607564632\t1\t"LCMSMS_2.mzML"\t389\t1\t479\t580\t576\t78.808182\t498.168731689453\t1.15793937994546\t79.36215\t1\t580\tTRUE\n+"840"\t498.169196251216\t498.168304443359\t498.216522216797\t81.344292\t69.864534\t93.704046\t47195241.5238887\t185121008.239345\t9710354\t12214248.0689462\t1\t17.5782472187331\t2\t"LCMSMS_1.mzML"\t778\t1\t1313\t586\t582\t79.776168\t498.168914794922\t0.564981329073345\t80.330904\t2\t586\tTRUE\n+"840"\t498.169196251216\t498.168304443359\t498.216522216797\t81.344292\t69.864534\t93.704046\t47195241.5238887\t185121008.239345\t9710354\t12214248.0689462\t1\t17.5782472187331\t2\t"LCMSMS_1.mzML"\t778\t1\t1372\t657\t654\t89.058666\t498.169708251953\t1.02776474439097\t89.521512\t2\t657\tTRUE\n+"843"\t499.250501059464\t499.216003417969\t499.255126953125\t129.271086\t116.806434\t134.058318\t55312967.4069412\t179331694.489759\t13120593\t14382850.9535263\t1\t18.1627514816931\t1\t"LCMSMS_2.mzML"\t391\t1\t778\t939\t936\t126.186204\t499.250396728516\t0.208975150626037\t126.64716\t1\t939\tTRUE\n+"843"\t499.250391260917\t499.216522216797\t499.254547119141\t129.525558\t116.993448\t134.305698\t60960211.430872\t197064903.836068\t13479257\t15776334.7230698\t1\t17.5991745757\t2\t"LCMSMS_1.mzML"\t780\t1\t1605\t937\t936\t126.441198\t499.250396728516\t0.0109516161922676\t126.711816\t2\t937\tTRUE\n' |
| b |
| diff -r a46824d13914 -r a8842e5e75a7 test-data/flagRemove_output.tsv --- a/test-data/flagRemove_output.tsv Wed Jun 12 16:09:13 2024 +0000 +++ b/test-data/flagRemove_output.tsv Thu Jun 13 11:43:16 2024 +0000 |
| b |
| @@ -1,7 +1,7 @@ "grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full" "grp_names" -"1" "1" "205" "205" "205" "2794.024" "2793.436" "2803.044" "3" "0" "3" NA NA NA "1507943.06947222" "1533767.074875" "1354004.93486208" NA "1507943.06947222" NA "6.63321894286696" "0" "1" NA "0.19255594131829" "0.19255594131829" "1" "0" "1" "1" "205" "205" "2767.512" "2816.3" "M205T2794" -"2" "2" "231" "231" "231" "2519.839" "2504.508" "2535.473" "6" "1" "3" NA NA "30766.3350000011" "45103.2999999989" "104989.362833335" "49776.3899999999" "30766.3350000011" "49776.3899999999" NA "49.9951594827002" "0.333333333333333" "1" NA "0.360049078987311" "0.432545161192324" "2" "0" "1" "1" "231" "231" "2507.963" "2514.738" "M231T2520" -"3" "3" "402.200012207031" "402.200012207031" "402.200012207031" "3598.551" "3592.212" "3610.036" "4" "1" "3" NA NA "14554.4999999997" "37458.7453333329" "91785.7281052629" "142007.379692308" "14554.4999999997" "91785.7281052629" NA "57.8293736085665" "0.333333333333333" "1" NA "0.251337522585405" "0.206331444617903" "3" "0" "1" "1" "402.200012207031" "402.200012207031" "3563.503" "3597.137" "M402T3599" -"4" "4" "449.100006103516" "449.100006103516" "449.100006103516" "2667.26" "2664.638" "2676.652" "3" "0" "3" NA NA NA "6663.76999999991" "11221.0499999998" "6830.35200000006" NA "6830.35200000006" NA "31.3702198972974" "0" "1" NA "0.236631537850627" "0.236631537850627" "4" "0" "1" "1" "449.100006103516" "449.100006103516" "2659.233" "2670.393" "M449T2667" -"5" "5" "564.200012207031" "564.200012207031" "564.200012207031" "3498.002" "3491.993" "3507.349" "4" "0" "3" NA NA NA "149980.21" "87237.7950000002" "160589.344999999" NA "149980.21" NA "29.896461605479" "0" "1" NA "0.135256683436928" "0.135256683436928" "5" "0" "1" "1" "564.200012207031" "564.200012207031" "3473.214" "3501.034" "M564T3498" -"6" "6" "586.299987792969" "586.299987792969" "586.299987792969" "3308.894" "3308.249" "3310.396" "3" "0" "3" NA NA NA "10504.2799999998" "7491.65500000026" "12363.4999999997" NA "10504.2799999998" NA "24.294650028749" "0" "1" NA "0.0332903660058522" "0.0332903660058522" "6" "0" "1" "1" "586.299987792969" "586.299987792969" "3304.199" "3312.024" "M586T3309" +"1" "1" 205 205 205 2794.024 2793.436 2803.044 3 0 3 NA NA NA 1507943.06947222 1533767.074875 1354004.93486208 NA 1507943.06947222 NA 6.63321894286696 0 1 NA 0.19255594131829 0.19255594131829 1 0 1 1 205 205 2767.512 2828.409 "M205T2794" +"2" "2" 231 231 231 2519.839 2504.508 2535.473 6 1 3 NA NA 30766.3350000011 45103.2999999989 104989.362833335 49776.3899999999 30766.3350000011 49776.3899999999 NA 49.9951594827002 0.333333333333333 1 NA 0.360049078987311 0.432545161192324 2 0 1 1 231 231 2507.963 2540.338 "M231T2520" +"3" "3" 402.200012207031 402.200012207031 402.200012207031 3598.551 3592.212 3610.036 4 1 3 NA NA 14554.4999999997 37458.7453333329 91785.7281052629 142007.379692308 14554.4999999997 91785.7281052629 NA 57.8293736085665 0.333333333333333 1 NA 0.251337522585405 0.206331444617903 3 0 1 1 402.200012207031 402.200012207031 3563.503 3618.754 "M402T3599" +"4" "4" 449.100006103516 449.100006103516 449.100006103516 2667.26 2664.638 2676.652 3 0 3 NA NA NA 6663.76999999991 11221.0499999998 6830.35200000006 NA 6830.35200000006 NA 31.3702198972974 0 1 NA 0.236631537850627 0.236631537850627 4 0 1 1 449.100006103516 449.100006103516 2659.233 2679.782 "M449T2667" +"5" "5" 564.200012207031 564.200012207031 564.200012207031 3498.002 3491.993 3507.349 4 0 3 NA NA NA 149980.21 87237.7950000002 160589.344999999 NA 149980.21 NA 29.896461605479 0 1 NA 0.135256683436928 0.135256683436928 5 0 1 1 564.200012207031 564.200012207031 3473.214 3521.727 "M564T3498" +"6" "6" 586.299987792969 586.299987792969 586.299987792969 3308.894 3308.249 3310.396 3 0 3 NA NA NA 10504.2799999998 7491.65500000026 12363.4999999997 NA 10504.2799999998 NA 24.294650028749 0 1 NA 0.0332903660058522 0.0332903660058522 6 0 1 1 586.299987792969 586.299987792969 3304.199 3315.151 "M586T3309" |
| b |
| diff -r a46824d13914 -r a8842e5e75a7 test-data/frag4feature_output.RData |
| b |
| Binary file test-data/frag4feature_output.RData has changed |
| b |
| diff -r a46824d13914 -r a8842e5e75a7 test-data/frag4feature_output.tsv --- a/test-data/frag4feature_output.tsv Wed Jun 12 16:09:13 2024 +0000 +++ b/test-data/frag4feature_output.tsv Thu Jun 13 11:43:16 2024 +0000 |
| b |
| b'@@ -1,324 +1,324 @@\n-"grpid"\t"mz"\t"mzmin"\t"mzmax"\t"rt"\t"rtmin"\t"rtmax"\t"into"\t"intf"\t"maxo"\t"maxf"\t"i"\t"sn"\t"sample"\t"cid"\t"filename"\t"inPurity"\t"pid"\t"precurMtchID"\t"precurMtchScan"\t"precurMtchRT"\t"precurMtchMZ"\t"precurMtchPPM"\t"retentionTime"\t"fileid"\t"seqNum"\n-"12"\t112.050766766484\t112.050651550293\t112.087196350098\t67.47903\t55.2769038\t80.361672\t36223791.266206\t133522503.549415\t7158012.5\t8555976.39592391\t1\t21.054952458659\t1\t9\t"LCMSMS_2.mzML"\t1\t384\t466\t462\t64.427298\t112.050704956055\t0.55162878935702\t64.958766\t1\t466\n-"12"\t112.05085569128\t112.050621032715\t112.120460510254\t67.634034\t55.4140188\t80.555406\t36139265.8017591\t133395720.51942\t7426335.5\t8522973.08164079\t1\t20.3803986860233\t2\t400\t"LCMSMS_1.mzML"\t1\t1218\t472\t468\t65.376156\t112.050743103027\t1.00479600749392\t65.928894\t2\t472\n-"14"\t113.03541992282\t113.034698486328\t113.059997558594\t83.441172\t72.006432\t95.851296\t88462324.9597518\t348004137.88132\t18599380\t22772249.3980656\t1\t27.431622141047\t1\t11\t"LCMSMS_2.mzML"\t1\t499\t604\t600\t81.93093\t113.034736633301\t6.04491512630164\t82.463394\t1\t604\n-"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t1\t1321\t596\t594\t81.344292\t113.034736633301\t5.61834418239318\t81.70764\t2\t596\n-"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t0.472133563046185\t1380\t667\t666\t90.601068\t113.034713745117\t5.8208310964319\t90.871572\t2\t667\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t0.950632241095866\t226\t277\t276\t40.9547952\t116.070838928223\t1.7359353575902\t41.2252842\t1\t277\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t281\t343\t342\t49.182402\t116.070831298828\t1.67020474130592\t49.452918\t1\t343\n-"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t337\t410\t408\t57.5697876\t116.070770263672\t1.14435981103166\t57.9341562\t1\t410\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t0.989376188689562\t1055\t277\t276\t41.0984136\t116.070816040039\t2.22463819204545\t41.3688786\t2\t277\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1110\t343\t342\t49.3156656\t116.070823669434\t2.29036885341395\t49.586265\t2\t343\n-"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1165\t409\t408\t57.7060356\t116.070785522461\t1.96171554657148\t57.976677\t2\t409\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t391\t475\t474\t65.949288\t132.101821899414\t0.0447061558976329\t66.21981\t1\t475\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t446\t541\t540\t74.297424\t132.101867675781\t0.301817188616646\t74.567904\t1\t541\n-"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t501\t607\t606\t82.686066\t132.101852416992\t0.186309407111886\t82.956534\t1\t607\n-"41"\t132.101827230045\t1'..b'13324101\t461.110168457031\t461.2431640625\t76.520544\t65.179668\t88.866054\t48904711.0742877\t195241268.75592\t14374106\t12850193.8354307\t1\t21.2071228333724\t1\t"LCMSMS_2.mzML"\t371\t1\t465\t563\t558\t76.520544\t461.209899902344\t6.04192381657049\t77.141778\t1\t563\n+"757"\t461.20738152051\t461.121826171875\t461.243560791016\t77.474424\t65.376156\t89.831544\t48607882.314214\t192672537.990574\t14159047\t12716867.2850009\t1\t20.5600686941203\t2\t"LCMSMS_1.mzML"\t761\t1\t1299\t569\t564\t77.474424\t461.209899902344\t5.460410945608\t78.102018\t2\t569\n+"759"\t462.22122959389\t462.213439941406\t462.291839599609\t57.7060356\t44.7995376\t75.972048\t38559454.0832874\t105979165.236253\t3445839.75\t5926579.6352243\t1\t10.2307809194678\t2\t"LCMSMS_1.mzML"\t762\t0.944176192726551\t1187\t435\t432\t60.766158\t462.218811035156\t5.23247003559527\t61.226112\t2\t435\n+"787"\t476.190702761819\t476.186126708984\t476.307098388672\t81.162672\t69.717042\t92.725812\t39151803.0473944\t118893746.090445\t7816689\t8198001.40019319\t1\t14.9845576620757\t1\t"LCMSMS_2.mzML"\t378\t0.977294138555063\t474\t574\t570\t78.035046\t476.186828613281\t8.13570805892727\t78.58677\t1\t574\n+"787"\t476.190794182677\t476.186218261719\t476.307495117188\t81.344292\t69.864534\t92.927058\t43745001.5410773\t135433069.148731\t8875996\t9304027.49811656\t1\t15.612354791168\t2\t"LCMSMS_1.mzML"\t768\t0.917917041077806\t1303\t574\t570\t78.227304\t476.186981201172\t8.00725581423595\t78.779022\t2\t574\n+"787"\t476.190794182677\t476.186218261719\t476.307495117188\t81.344292\t69.864534\t92.927058\t43745001.5410773\t135433069.148731\t8875996\t9304027.49811656\t1\t15.612354791168\t2\t"LCMSMS_1.mzML"\t768\t0.990314571321696\t1309\t581\t576\t78.998916\t476.187042236328\t7.87908207170328\t79.648392\t2\t581\n+"812"\t487.181176540989\t487.099060058594\t487.239410400391\t66.710418\t54.5086626\t79.585674\t58453273.9503532\t230378509.09492\t15813294\t14998690.3403142\t1\t19.4416133244468\t1\t"LCMSMS_2.mzML"\t384\t1\t394\t478\t474\t65.949288\t487.177612304688\t7.31603861859596\t66.493134\t1\t478\n+"812"\t487.180877999963\t487.099700927734\t487.239501953125\t66.865908\t54.6427758\t78.998916\t60132074.4709007\t238189012.918308\t18110170\t15528706.5784369\t1\t19.1064097764383\t2\t"LCMSMS_1.mzML"\t774\t1\t1224\t479\t474\t66.147648\t487.177856445312\t6.20212078776047\t66.74139\t2\t479\n+"830"\t494.196757645669\t494.119018554688\t494.198516845703\t49.9356528\t37.8964158\t62.153292\t31096636.998985\t121560345.75829\t6061495.5\t8000920.55155143\t1\t19.2246142395834\t1\t"LCMSMS_2.mzML"\t387\t1\t280\t341\t336\t48.4095336\t494.197631835938\t1.76891138083971\t49.060251\t1\t341\n+"830"\t494.1970608933\t494.119293212891\t494.197875976562\t50.0837946\t38.0417766\t62.309778\t31975460.900009\t125089224.818786\t5749075.5\t8239138.02501223\t1\t18.9671855740286\t2\t"LCMSMS_1.mzML"\t776\t1\t1112\t345\t342\t49.3156656\t494.197631835938\t1.15529347093956\t49.7757558\t2\t345\n+"840"\t498.169308539313\t498.16845703125\t498.28955078125\t81.162672\t68.984166\t93.504684\t46040504.6258466\t180736904.384221\t9105023\t11919892.2978446\t1\t18.9934607564632\t1\t"LCMSMS_2.mzML"\t389\t1\t479\t580\t576\t78.808182\t498.168731689453\t1.15793937994546\t79.36215\t1\t580\n+"840"\t498.169196251216\t498.168304443359\t498.216522216797\t81.344292\t69.864534\t93.704046\t47195241.5238887\t185121008.239345\t9710354\t12214248.0689462\t1\t17.5782472187331\t2\t"LCMSMS_1.mzML"\t778\t1\t1313\t586\t582\t79.776168\t498.168914794922\t0.564981329073345\t80.330904\t2\t586\n+"840"\t498.169196251216\t498.168304443359\t498.216522216797\t81.344292\t69.864534\t93.704046\t47195241.5238887\t185121008.239345\t9710354\t12214248.0689462\t1\t17.5782472187331\t2\t"LCMSMS_1.mzML"\t778\t1\t1372\t657\t654\t89.058666\t498.169708251953\t1.02776474439097\t89.521512\t2\t657\n+"843"\t499.250501059464\t499.216003417969\t499.255126953125\t129.271086\t116.806434\t134.058318\t55312967.4069412\t179331694.489759\t13120593\t14382850.9535263\t1\t18.1627514816931\t1\t"LCMSMS_2.mzML"\t391\t1\t778\t939\t936\t126.186204\t499.250396728516\t0.208975150626037\t126.64716\t1\t939\n+"843"\t499.250391260917\t499.216522216797\t499.254547119141\t129.525558\t116.993448\t134.305698\t60960211.430872\t197064903.836068\t13479257\t15776334.7230698\t1\t17.5991745757\t2\t"LCMSMS_1.mzML"\t780\t1\t1605\t937\t936\t126.441198\t499.250396728516\t0.0109516161922676\t126.711816\t2\t937\n' 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