Mercurial > repos > computational-metabolomics > dimspy_merge_peaklists
changeset 1:50ec7a43cb62 draft
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4"
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--- a/README.rst Sat Apr 11 16:46:21 2020 -0400 +++ b/README.rst Tue Apr 28 17:21:19 2020 -0400 @@ -1,6 +1,6 @@ Galaxy tool wrappers for DIMSpy -======================== -|Build Status (Travis)| |Git| |Bioconda| |License| +=============================== +|Build Status (Travis)| |galaxy-eu| |Git| |Bioconda| |License| Galaxy tool wrappers for Python package DIMSpy: data processing of direct-infusion mass spectrometry (DIMS)-based metabolomics and lipidomics data @@ -11,7 +11,7 @@ Version -------- -v1.4.0+Galaxy0 (`DIMSpy v1.4.0 <https://pypi.org/project/dimspy/1.4.0/>`_) +v2.0.0+Galaxy0 (`DIMSpy v2.0.0 <https://pypi.org/project/dimspy/2.0.0/>`_) Galaxy @@ -19,11 +19,19 @@ `Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. -Authors, contributors & Contacts ----------------------------------- - - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ - - Thomas N. Lawson (tnl495@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ - - Martin R. Jones (m.r.jones.1@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ +Credits +------- + +**Authors and contributors** + - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`__ + - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`__ + - Martin R. Jones (martin.jones@eawag.ch) - `Eawag (Switzerland) <https://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/martin-jones/show/>`_ + + +**DIMSpy acknowledges support from the following funders:** + - BBSRC, grant number BB/M019985/1 + - European Commission's H2020 programme, grant agreement number 654241 + - Wellcome Trust, grant number 202952/Z/16/Z Bugs @@ -36,8 +44,10 @@ Changes ------- +v2.0.0+galaxy0 + - First release (Python 3-based version `DIMSpy <https://pypi.org/project/dimspy/2.0.0/>`_) + v1.4.0+galaxy0 - - First stable release - Final release (Python 2-based version `DIMSpy <https://pypi.org/project/dimspy/1.4.0/>`_) @@ -59,6 +69,9 @@ .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 :target: https://github.com/computational-metabolomics/dimspy +.. |galaxy-eu| image:: https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAASCAYAAABB7B6eAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAACXBIWXMAAAsTAAALEwEAmpwYAAACC2lUWHRYTUw6Y29tLmFkb2JlLnhtcAAAAAAAPHg6eG1wbWV0YSB4bWxuczp4PSJhZG9iZTpuczptZXRhLyIgeDp4bXB0az0iWE1QIENvcmUgNS40LjAiPgogICA8cmRmOlJERiB4bWxuczpyZGY9Imh0dHA6Ly93d3cudzMub3JnLzE5OTkvMDIvMjItcmRmLXN5bnRheC1ucyMiPgogICAgICA8cmRmOkRlc2NyaXB0aW9uIHJkZjphYm91dD0iIgogICAgICAgICAgICB4bWxuczp0aWZmPSJodHRwOi8vbnMuYWRvYmUuY29tL3RpZmYvMS4wLyI+CiAgICAgICAgIDx0aWZmOlJlc29sdXRpb25Vbml0PjI8L3RpZmY6UmVzb2x1dGlvblVuaXQ+CiAgICAgICAgIDx0aWZmOkNvbXByZXNzaW9uPjE8L3RpZmY6Q29tcHJlc3Npb24+CiAgICAgICAgIDx0aWZmOk9yaWVudGF0aW9uPjE8L3RpZmY6T3JpZW50YXRpb24+CiAgICAgICAgIDx0aWZmOlBob3RvbWV0cmljSW50ZXJwcmV0YXRpb24+MjwvdGlmZjpQaG90b21ldHJpY0ludGVycHJldGF0aW9uPgogICAgICA8L3JkZjpEZXNjcmlwdGlvbj4KICAgPC9yZGY6UkRGPgo8L3g6eG1wbWV0YT4KD0UqkwAAAn9JREFUOBGlVEuLE0EQruqZiftwDz4QYT1IYM8eFkHFw/4HYX+GB3/B4l/YP+CP8OBNTwpCwFMQXAQPKtnsg5nJZpKdni6/6kzHvAYDFtRUT71f3UwAEbkLch9ogQxcBwRKMfAnM1/CBwgrbxkgPAYqlBOy1jfovlaPsEiWPROZmqmZKKzOYCJb/AbdYLso9/9B6GppBRqCrjSYYaquZq20EUKAzVpjo1FzWRDVrNay6C/HDxT92wXrAVCH3ASqq5VqEtv1WZ13Mdwf8LFyyKECNbgHHAObWhScf4Wnj9CbQpPzWYU3UFoX3qkhlG8AY2BTQt5/EA7qaEPQsgGLWied0A8VKrHAsCC1eJ6EFoUd1v6GoPOaRAtDPViUr/wPzkIFV9AaAZGtYB568VyJfijV+ZBzlVZJ3W7XHB2RESGe4opXIGzRTdjcAupOK09RA6kzr1NTrTj7V1ugM4VgPGWEw+e39CxO6JUw5XhhKihmaDacU2GiR0Ohcc4cZ+Kq3AjlEnEeRSazLs6/9b/kh4eTC+hngE3QQD7Yyclxsrf3cpxsPXn+cFdenF9aqlBXMXaDiEyfyfawBz2RqC/O9WF1ysacOpytlUSoqNrtfbS642+4D4CS9V3xb4u8P/ACI4O810efRu6KsC0QnjHJGaq4IOGUjWTo/YDZDB3xSIxcGyNlWcTucb4T3in/3IaueNrZyX0lGOrWndstOr+w21UlVFokILjJLFhPukbVY8OmwNQ3nZgNJNmKDccusSb4UIe+gtkI+9/bSLJDjqn763f5CQ5TLApmICkqwR0QnUPKZFIUnoozWcQuRbC0Km02knj0tPYx63furGs3x/iPnz83zJDVNtdP3QAAAABJRU5ErkJggg== + :target: http://usegalaxy.eu + .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 :target: http://bioconda.github.io/recipes/dimspy/README.html
--- a/macros.xml Sat Apr 11 16:46:21 2020 -0400 +++ b/macros.xml Tue Apr 28 17:21:19 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.4.0</token> + <token name="@TOOL_VERSION@">2.0.0</token> <token name="@GALAXY_TOOL_VERSION@">0</token> <xml name="requirements"> @@ -7,6 +7,7 @@ <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement> </requirements> </xml> + <token name="@HDF5_PM_TO_TXT@"> dimspy hdf5-pm-to-txt
--- a/merge_peaklists.xml Sat Apr 11 16:46:21 2020 -0400 +++ b/merge_peaklists.xml Tue Apr 28 17:21:19 2020 -0400 @@ -10,52 +10,60 @@ #for $fn in $hdf5_files_in --input '$fn' #end for - #if $multilist.flag == 'true' + + #if $multilist --output . - --filelist $multilist.filelist' #else --output '$hdf5_file_out' - #if $filelist - --filelist '$multilist.filelist' - #end if + #end if + + #if $filelist + --filelist '$filelist' #end if ]]> </command> <inputs> - <param name="hdf5_files_in" argument="--input" type="data" format="h5" multiple="true" min="2" label="Peaklist to merge" help="Select a minimum of two hdf5 files" /> - <conditional name="multilist"> - <param name="flag" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create multiple merged peaklists?" help="Based on a 'multilist' column in the filelist text file, divide the peaklists into different lists - e.g. [pl1, pl2, pl3, pl4] can be converted to 2 new lists: + <param name="hdf5_files_in" type="data" multiple="true" format="h5" min="2" label="Peaklist to merge" help="Select a minimum of two hdf5 files" argument="--input" /> + <param name="multilist" type="boolean" checked="false" label="Create multiple merged peaklists?" + help="Based on a 'multilist' column in the filelist text file, divide the peaklists into different lists + e.g. [pl1 pl2], [pl3, pl4] can be converted to 2 new lists: [pl1, pl3] [pl2, pl4]"/> - <when value="true"> - <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" label="Filelist" /> - </when> - <when value="false"> - <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist" /> - </when> - </conditional> + <param type="data" format="tsv,tabular" optional="true" label="Filelist" + help="A table containing metadata for each experimental sample. See help section below for more details." argument="--filelist" /> </inputs> <outputs> <collection name="multiple_merged" type="list" label="${tool.name} on ${on_string}: Peaklists (HDF5)"> - <filter>multilist["flag"] is True</filter> + <filter>multilist</filter> <discover_datasets pattern="(?P<designation>.+)\.hdf5" format="h5" directory="." visible="false" /> </collection> <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)"> - <filter>multilist["flag"] is False</filter> + <filter>multilist is False</filter> </data> </outputs> <tests> <test> + <!-- Merge (no filelist) --> <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" /> <output name="hdf5_file_out" value="merged_01.h5" ftype="h5" compare="sim_size" /> </test> <test> + <!-- Merge (with filelist) --> <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" /> - <conditional name="multilist"> - <param name="filelist" value="filelist_merge.txt" ftype="tsv"/> - </conditional> + <param name="filelist" value="filelist_merge.txt" ftype="tsv"/> <output name="hdf5_file_out" value="merged_02.h5" ftype="h5" compare="sim_size" /> </test> + <test> + <!-- Merge (multilist) --> + <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" /> + <param name="filelist" value="filelist_multilist_merge.txt" ftype="tsv"/> + <param name="multilist" value="true"/> + <output_collection name="multiple_merged" type="list"> + <element name="merged_peaklist_001" file="merged_peaklist_001.h5" ftype="h5" compare="sim_size" /> + <element name="merged_peaklist_002" file="merged_peaklist_002.h5" ftype="h5" compare="sim_size" /> + <element name="merged_peaklist_003" file="merged_peaklist_003.h5" ftype="h5" compare="sim_size" /> + </output_collection> + </test> + </tests> <help> --------------- @@ -77,51 +85,59 @@ Parameters ---------- +| + **Peaklist to merge** (REQUIRED; minimally requires two .hdf5 files) - selection menu from which the user must select two or more .hdf5 files from the active Galaxy history. -**NOTE**: if a .hdf5 file containing a peak intensity matrix is selected, then the peaklists used in generating that matrix are extracted from the file e.g. [pl1, pl2, pl3] + [pm456] = [pl1, pl2, pl3] + [pl4, pl5, pl6] = [pl1, pl2, pl3, pl4, pl5, pl6] . + **NOTE**: if a .hdf5 file containing a peak intensity matrix is selected, then the peaklists used in generating that matrix are extracted from the file e.g. [pl1, pl2, pl3] + [pm456] = [pl1, pl2, pl3] + [pl4, pl5, pl6] = [pl1, pl2, pl3, pl4, pl5, pl6] . | **Create multiple merged peaklists** (REQUIRED; default = “No”) - binary toggle: - - **No** - all extracted peaklists are exported to a single .hdf5 file in the active Galaxy history. Metadata associated with each peaklist is also captured in this file. + **No** - all extracted peaklists are exported to a single .hdf5 file in the active Galaxy history. Metadata associated with each peaklist is also captured in this file. + + **Yes** - multiple .hdf5 files are exported to the active Galaxy history, each of which containing a user-defined subset of the extracted peaklist(s) in accordance with the “multilist” column of the input “Filelist”, e.g. using the mock filelist shown below, two .hdf5 files would be exported to history: + + * The first .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank1_rep1.raw and blank1_rep2.raw], i.e. all filenames associated with multilist value '1' - - **Yes** - multiple .hdf5 files are exported to the active Galaxy history, each of which containing a user-defined subset of the extracted peaklist(s) in accordance with the “multilist” column of the input “Filelist”, e.g. using the mock filelist shown below, two .hdf5 files would be exported to history: - - The first .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank1_rep1.raw and blank1_rep2.raw], i.e. all filenames associated with multilist value '1' + * The second .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank_rep3.raw and blank_rep4.raw], i.e. all filenames associated with multilist value '2' + + | + + + **NOTE** - if for each analysed study sample a corresponding blank sample has been analysed, then the multilist column can be used to pair these together in an output .hdf5 file. This enables sample-specific blank filtering at a later stage. - The second .hdf5 file would contain peaklists from [blank_rep1.raw, blank_rep2.raw, blank_rep3.raw and blank_rep4.raw], i.e. all filenames associated with multilist value '2' - - **NOTE** - if for each analysed study sample a corresponding blank sample has been analysed, then the multilist column can be used to pair these together in an output .hdf5 file. This enables sample-specific blank filtering at a later stage. | **Filelist / Samplelist** (OPTIONAL) - a selection menu from which one or more filelists can be selected. -**Mock example of a filelist** - the optional multilist column determines which peaklists are exported together in .hdf5 format. - -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| filename | classLabel | replicate | batch | injectionOrder | multilist | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| sample_rep1.raw | sample | 1 | 1 | 1 | 1 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| sample_rep2.raw | sample | 2 | 1 | 2 | 1 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| sample_rep3.raw | sample | 3 | 1 | 3 | 2 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| sample_rep4.raw | sample | 4 | 1 | 4 | 2 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| blank_rep1.raw | blank | 1 | 1 | 5 | 1 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| blank_rep2.raw | blank | 2 | 1 | 6 | 1 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| blank_rep3.raw | blank | 3 | 1 | 7 | 2 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| blank_rep4.raw | blank | 4 | 1 | 8 | 2 | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ -| ... | ... | ... | ... | ... | ... | [...] | -+-----------------+------------+-----------+-------+----------------+-----------+-------+ + **Mock example of a filelist** - the optional multilist column determines which peaklists are exported together in .hdf5 format. + + | + + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | filename | classLabel | replicate | batch | injectionOrder | multilist | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | sample_rep1.raw | sample | 1 | 1 | 1 | 1 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | sample_rep2.raw | sample | 2 | 1 | 2 | 1 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | sample_rep3.raw | sample | 3 | 1 | 3 | 2 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | sample_rep4.raw | sample | 4 | 1 | 4 | 2 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | blank_rep1.raw | blank | 1 | 1 | 5 | 1 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | blank_rep2.raw | blank | 2 | 1 | 6 | 1 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | blank_rep3.raw | blank | 3 | 1 | 7 | 2 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | blank_rep4.raw | blank | 4 | 1 | 8 | 2 | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ + | ... | ... | ... | ... | ... | ... | [...] | + +-----------------+------------+-----------+-------+----------------+-----------+-------+ | @@ -130,12 +146,16 @@ Output file(s) -------------- +| + One or more .hdf5 file(s), each containing one or more peaklists. +| + ----------------------------------- @github_developers_contributors@ -@license@ + </help> <expand macro="citations" /> -</tool> +</tool> \ No newline at end of file
--- a/test-data/batch04_QC17_rep01_262.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep01_262.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,499 +1,499 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags -97.0050038629 24371.8476562 10.2138983463 1 0.1 nan 1.0 1.0 1 0 0 -98.9955018467 82339.6554688 34.2217993561 10 1.0 6.92819640371 10.0 1.0 1 1 1 -101.752289053 26659.7988281 11.3852899456 1 0.1 nan 1.0 1.0 1 0 0 -101.753170732 27749.7890625 11.6295460489 1 0.1 nan 1.0 1.0 1 0 0 -101.760001089 27966.8964844 12.0169301401 1 0.1 nan 1.0 1.0 1 0 0 -101.760785449 27373.5214844 10.900619804 1 0.1 nan 1.0 1.0 1 0 0 -101.761942982 31181.6132812 13.3163686068 1 0.1 nan 1.0 1.0 1 0 0 -101.762415519 29687.0507812 11.8219080382 1 0.1 nan 1.0 1.0 1 0 0 -101.762823343 33850.9179688 14.186443307 1 0.1 nan 1.0 1.0 1 0 0 -101.763862658 24648.4902344 10.1551295314 1 0.1 nan 1.0 1.0 1 0 0 -101.769632024 30046.4433594 12.9104783225 1 0.1 nan 1.0 1.0 1 0 0 -101.770656275 29317.1523438 12.0786091445 1 0.1 nan 1.0 1.0 1 0 0 -101.771230198 26653.9208984 11.1798351166 2 0.2 12.3745639478 2.0 1.0 1 0 0 -101.771924703 28194.547526 11.6732716145 3 0.3 12.9357310009 3.0 1.0 1 0 0 -101.77247223 34544.1826172 14.3379527656 2 0.2 12.9547876966 2.0 1.0 1 0 0 -101.773679514 25715.6894531 10.5357634836 1 0.1 nan 1.0 1.0 1 0 0 -101.773953634 30085.4492188 12.417921349 1 0.1 nan 1.0 1.0 1 0 0 -101.774167342 26579.9921875 11.0441488074 2 0.2 5.16123631347 2.0 1.0 1 0 0 -101.774444231 29461.8509115 12.0906833959 3 0.3 20.528388653 3.0 1.0 1 0 0 -101.774765704 27428.7265625 11.5314577636 1 0.1 nan 1.0 1.0 1 0 0 -101.775561023 24917.1816406 10.4206324468 2 0.2 2.75965479961 2.0 1.0 1 0 0 -101.776071685 29167.1809896 12.3954657742 3 0.3 23.4812227967 3.0 1.0 1 0 0 -101.776393302 28083.9746094 11.6515532862 2 0.2 4.85365856211 2.0 1.0 1 0 0 -101.776905074 26652.5761719 11.3388946781 2 0.2 11.7068108415 2.0 1.0 1 0 0 -101.777138532 32581.8847656 13.9143662495 1 0.1 nan 1.0 1.0 1 0 0 -101.777438306 28769.8789062 12.0600745322 4 0.4 9.13554703544 4.0 1.0 1 0 0 -101.777967579 32452.6503906 13.138204625 2 0.2 21.7364211663 2.0 1.0 1 0 0 -101.778480696 23612.796875 10.1460428625 1 0.1 nan 1.0 1.0 1 0 0 -101.778943527 27877.5598958 11.6093674297 3 0.3 10.3704940078 3.0 1.0 1 0 0 -101.779427021 34463.3793945 14.3282799491 4 0.4 38.3692135574 4.0 1.0 1 0 0 -101.779717111 24811.1035156 10.3249024942 2 0.2 2.22770098363 2.0 1.0 1 0 0 -101.780041288 25475.5019531 10.6764243294 1 0.1 nan 1.0 1.0 1 0 0 -101.780514162 31097.784375 12.9298184227 5 0.5 20.5747845219 5.0 1.0 1 1 1 -101.780918614 39182.8179688 16.3508209469 5 0.5 24.1922484454 5.0 1.0 1 1 1 -101.781243875 38214.7174479 15.8049003965 3 0.3 27.9776080666 3.0 1.0 1 0 0 -101.781590623 40594.796875 16.7655466701 5 0.5 21.1439967691 5.0 1.0 1 1 1 -101.781838147 30143.6171875 12.432025129 2 0.2 18.6464498566 2.0 1.0 1 0 0 -101.78211636 36808.7841797 15.285422144 2 0.2 19.4768339755 2.0 1.0 1 0 0 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--- a/test-data/batch04_QC17_rep01_262_2_263_3_264.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep01_262_2_263_3_264.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,436 +1,436 @@ mz intensity snr present fraction rsd occurrence purity present_flag flags -98.9955011572 84070.4861979 32.5719724663 3 1.0 1.87384937773 3.0 1.0 1 1 -101.772204612 29348.18125 11.0363579242 1 0.333333333333 nan 1.0 1.0 0 0 -101.775137765 32479.0789063 12.137428113 1 0.333333333333 nan 1.0 1.0 0 0 -101.779872302 40495.5066406 15.0839046164 1 0.333333333333 nan 1.0 1.0 0 0 -101.780514162 31097.784375 12.9298184227 1 0.333333333333 nan 1.0 1.0 0 0 -101.780918614 39182.8179688 16.3508209469 1 0.333333333333 nan 1.0 1.0 0 0 -101.781524007 40012.0361328 15.7096977432 2 0.666666666667 2.05975057731 2.0 1.0 1 1 -101.781813314 42852.5403646 16.0113159229 1 0.333333333333 nan 1.0 1.0 0 0 -101.782467224 37896.9567057 14.3413984371 1 0.333333333333 nan 1.0 1.0 0 0 -101.784935333 29937.0722656 11.2726505855 1 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--- a/test-data/batch04_QC17_rep01_262_scan5.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep01_262_scan5.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,16 +1,16 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags -118.086253583 259112.28125 108.590310357 1 1.0 nan 1.0 1.0 1 1 1 -132.075569347 292439.75 122.557383463 1 1.0 nan 1.0 1.0 1 1 1 -132.07609471 1416429.125 593.605511635 1 1.0 nan 1.0 1.0 1 1 1 -132.076675568 13824452.0 5793.63326953 1 1.0 nan 1.0 1.0 1 1 1 -132.077210117 1575695.125 660.351650744 1 1.0 nan 1.0 1.0 1 1 1 -132.10191987 313542.46875 131.401235894 1 1.0 nan 1.0 1.0 1 1 1 -133.080118521 416953.09375 174.739173443 1 1.0 nan 1.0 1.0 1 1 1 -136.04814365 456499.09375 191.312345477 1 1.0 nan 1.0 1.0 1 1 1 -140.068182551 1010273.5625 423.391431575 1 1.0 nan 1.0 1.0 1 1 1 -146.117590681 349931.4375 146.651340563 1 1.0 nan 1.0 1.0 1 1 1 -147.075656347 265543.125 111.285386466 1 1.0 nan 1.0 1.0 1 1 1 -147.076406922 1787055.75 748.929914018 1 1.0 nan 1.0 1.0 1 1 1 -148.003903094 628156.9375 263.251731901 1 1.0 nan 1.0 1.0 1 1 1 -148.060455078 628223.0 263.279417765 1 1.0 nan 1.0 1.0 1 1 1 -156.042176052 358481.28125 150.23445975 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file +118.08625358315543 259112.28125 108.59031035686559 1 1.0 nan 1.0 1.0 1 1 1 +132.07556934683342 292439.75 122.55738346321314 1 1.0 nan 1.0 1.0 1 1 1 +132.0760947095863 1416429.125 593.6055116347502 1 1.0 nan 1.0 1.0 1 1 1 +132.07667556766077 13824452.0 5793.6332695291385 1 1.0 nan 1.0 1.0 1 1 1 +132.07721011678618 1575695.125 660.3516507442663 1 1.0 nan 1.0 1.0 1 1 1 +132.10191987007823 313542.46875 131.40123589421844 1 1.0 nan 1.0 1.0 1 1 1 +133.08011852067256 416953.09375 174.7391734430487 1 1.0 nan 1.0 1.0 1 1 1 +136.04814364993567 456499.09375 191.31234547741212 1 1.0 nan 1.0 1.0 1 1 1 +140.06818255116025 1010273.5625 423.3914315754234 1 1.0 nan 1.0 1.0 1 1 1 +146.11759068119005 349931.4375 146.65134056338408 1 1.0 nan 1.0 1.0 1 1 1 +147.0756563467944 265543.125 111.28538646557091 1 1.0 nan 1.0 1.0 1 1 1 +147.07640692191154 1787055.75 748.9299140178103 1 1.0 nan 1.0 1.0 1 1 1 +148.0039030938299 628156.9375 263.25173190123814 1 1.0 nan 1.0 1.0 1 1 1 +148.06045507805527 628223.0 263.2794177652325 1 1.0 nan 1.0 1.0 1 1 1 +156.04217605179727 358481.28125 150.23445974953887 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file
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--- a/test-data/batch04_QC17_rep02_263_scan5.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep02_263_scan5.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,16 +1,16 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags -118.086250677 337163.65625 122.712121131 1 1.0 nan 1.0 1.0 1 1 1 -132.075550122 332844.34375 121.140089304 1 1.0 nan 1.0 1.0 1 1 1 -132.076099853 1704481.875 620.353298566 1 1.0 nan 1.0 1.0 1 1 1 -132.076679466 16160045.0 5881.51588337 1 1.0 nan 1.0 1.0 1 1 1 -132.077214638 1822359.625 663.255398091 1 1.0 nan 1.0 1.0 1 1 1 -132.101933824 282666.40625 102.877619342 1 1.0 nan 1.0 1.0 1 1 1 -133.080131913 404403.65625 147.184400014 1 1.0 nan 1.0 1.0 1 1 1 -136.048154103 493627.65625 179.657847531 1 1.0 nan 1.0 1.0 1 1 1 -140.068179697 1347873.625 490.564236313 1 1.0 nan 1.0 1.0 1 1 1 -146.117584879 372159.3125 135.448936411 1 1.0 nan 1.0 1.0 1 1 1 -147.075632546 385539.5625 140.318734292 1 1.0 nan 1.0 1.0 1 1 1 -147.076382858 2844217.0 1035.16465834 1 1.0 nan 1.0 1.0 1 1 1 -148.003894141 682524.0 248.407460918 1 1.0 nan 1.0 1.0 1 1 1 -148.060455449 776103.0625 282.465951625 1 1.0 nan 1.0 1.0 1 1 1 -156.042166366 644582.6875 234.598561741 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file +118.08625067696138 337163.65625 122.71212113134303 1 1.0 nan 1.0 1.0 1 1 1 +132.07555012249767 332844.34375 121.14008930383456 1 1.0 nan 1.0 1.0 1 1 1 +132.07609985276392 1704481.875 620.3532985657575 1 1.0 nan 1.0 1.0 1 1 1 +132.07667946555688 16160045.0 5881.515883365481 1 1.0 nan 1.0 1.0 1 1 1 +132.07721463819422 1822359.625 663.2553980908755 1 1.0 nan 1.0 1.0 1 1 1 +132.1019338237196 282666.40625 102.87761934160547 1 1.0 nan 1.0 1.0 1 1 1 +133.08013191302553 404403.65625 147.18440001407478 1 1.0 nan 1.0 1.0 1 1 1 +136.0481541025354 493627.65625 179.65784753092277 1 1.0 nan 1.0 1.0 1 1 1 +140.068179697104 1347873.625 490.5642363128883 1 1.0 nan 1.0 1.0 1 1 1 +146.1175848792974 372159.3125 135.44893641144736 1 1.0 nan 1.0 1.0 1 1 1 +147.0756325460884 385539.5625 140.31873429248054 1 1.0 nan 1.0 1.0 1 1 1 +147.07638285818732 2844217.0 1035.1646583433474 1 1.0 nan 1.0 1.0 1 1 1 +148.00389414102017 682524.0 248.40746091846538 1 1.0 nan 1.0 1.0 1 1 1 +148.0604554487374 776103.0625 282.4659516246609 1 1.0 nan 1.0 1.0 1 1 1 +156.0421663663729 644582.6875 234.5985617412364 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file
--- a/test-data/batch04_QC17_rep03_264.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep03_264.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,521 +1,521 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags -98.9954997246 85420.5765625 31.7500402338 10 1.0 7.05084168152 10.0 1.0 1 1 1 -101.75139692 28253.2851562 10.127417772 1 0.1 nan 1.0 1.0 1 0 0 -101.756447902 26853.5292969 10.2665688721 1 0.1 nan 1.0 1.0 1 0 0 -101.756740955 31525.3886719 12.052701544 1 0.1 nan 1.0 1.0 1 0 0 -101.758085047 28712.5615234 10.6823629006 2 0.2 4.91839023478 2.0 1.0 1 0 0 -101.760442484 29141.4121094 10.9411002292 1 0.1 nan 1.0 1.0 1 0 0 -101.761256844 32001.2285156 11.7395649133 1 0.1 nan 1.0 1.0 1 0 0 -101.766362618 33112.40625 12.6594458229 1 0.1 nan 1.0 1.0 1 0 0 -101.767750171 27310.8867188 10.2976928149 1 0.1 nan 1.0 1.0 1 0 0 -101.769490326 34806.9726562 12.7628240908 1 0.1 nan 1.0 1.0 1 0 0 -101.769873385 28806.4306641 10.8876126482 2 0.2 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--- a/test-data/batch04_QC17_rep03_264_scan5.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC17_rep03_264_scan5.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,16 +1,16 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag flags -118.086251246 317588.40625 119.748138639 1 1.0 nan 1.0 1.0 1 1 1 -132.075558769 336786.0625 126.986701372 1 1.0 nan 1.0 1.0 1 1 1 -132.076089225 1503678.875 566.968890702 1 1.0 nan 1.0 1.0 1 1 1 -132.076675013 16059164.0 6055.18009867 1 1.0 nan 1.0 1.0 1 1 1 -132.077209793 1795780.75 677.10721797 1 1.0 nan 1.0 1.0 1 1 1 -132.101921999 285028.125 107.471137978 1 1.0 nan 1.0 1.0 1 1 1 -133.08011769 461302.875 173.93632621 1 1.0 nan 1.0 1.0 1 1 1 -136.04813844 506052.625 190.80942095 1 1.0 nan 1.0 1.0 1 1 1 -140.068171152 1307694.5 493.072099615 1 1.0 nan 1.0 1.0 1 1 1 -146.117584259 391558.0 147.638707038 1 1.0 nan 1.0 1.0 1 1 1 -147.075637569 322906.625 121.753396966 1 1.0 nan 1.0 1.0 1 1 1 -147.07639398 2336210.5 880.878688697 1 1.0 nan 1.0 1.0 1 1 1 -148.003903003 731813.9375 275.933740404 1 1.0 nan 1.0 1.0 1 1 1 -148.060453166 780531.875 294.303058109 1 1.0 nan 1.0 1.0 1 1 1 -156.042166811 522879.53125 197.154081721 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file +118.08625124582368 317588.40625 119.74813863859575 1 1.0 nan 1.0 1.0 1 1 1 +132.07555876901927 336786.0625 126.98670137237345 1 1.0 nan 1.0 1.0 1 1 1 +132.07608922473702 1503678.875 566.9688907021545 1 1.0 nan 1.0 1.0 1 1 1 +132.07667501282035 16059164.0 6055.1800986656635 1 1.0 nan 1.0 1.0 1 1 1 +132.07720979273736 1795780.75 677.107217970182 1 1.0 nan 1.0 1.0 1 1 1 +132.10192199854097 285028.125 107.47113797829009 1 1.0 nan 1.0 1.0 1 1 1 +133.08011768986054 461302.875 173.9363262095869 1 1.0 nan 1.0 1.0 1 1 1 +136.04813844032049 506052.625 190.80942094977783 1 1.0 nan 1.0 1.0 1 1 1 +140.0681711521587 1307694.5 493.07209961455936 1 1.0 nan 1.0 1.0 1 1 1 +146.11758425867885 391558.0 147.63870703813285 1 1.0 nan 1.0 1.0 1 1 1 +147.07563756894905 322906.625 121.75339696557656 1 1.0 nan 1.0 1.0 1 1 1 +147.07639398009738 2336210.5 880.8786886972298 1 1.0 nan 1.0 1.0 1 1 1 +148.003903002935 731813.9375 275.9337404036821 1 1.0 nan 1.0 1.0 1 1 1 +148.06045316588452 780531.875 294.3030581090146 1 1.0 nan 1.0 1.0 1 1 1 +156.04216681053924 522879.53125 197.15408172085614 1 1.0 nan 1.0 1.0 1 1 1 \ No newline at end of file
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--- a/test-data/batch04_QC18_rep02_281.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC18_rep02_281.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,502 +1,502 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag rsd_flag flags -98.9955003428 105195.025 39.8878170701 10 1.0 6.59810533669 10.0 1.0 1 1 1 1 -101.75276154 30539.2851562 10.905372815 1 0.1 nan 1.0 1.0 1 0 0 0 -101.754367433 28890.609375 11.6182835689 1 0.1 nan 1.0 1.0 1 0 0 0 -101.764014372 34162.859375 13.7385052212 1 0.1 nan 1.0 1.0 1 0 0 0 -101.766739909 30527.2636719 10.9860538077 1 0.1 nan 1.0 1.0 1 0 0 0 -101.773634898 26218.9941406 10.5439004371 1 0.1 nan 1.0 1.0 1 0 0 0 -101.774158597 27432.5058594 10.7123940664 1 0.1 nan 1.0 1.0 1 0 0 0 -101.77479808 28445.8359375 11.1080994814 1 0.1 nan 1.0 1.0 1 0 0 0 -101.77622332 24926.2285156 10.1709657094 1 0.1 nan 1.0 1.0 1 0 0 0 -101.776969969 44213.7421875 15.9114998296 1 0.1 nan 1.0 1.0 1 0 0 0 -101.777243997 50399.2695312 17.9972393274 1 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--- a/test-data/batch04_QC18_rep03_282.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_QC18_rep03_282.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,516 +1,516 @@ mz intensity snr present fraction rsd occurrence purity snr_flag fraction_flag rsd_flag flags -98.9955018765 82253.4171875 32.3056045472 10 1.0 6.15287346541 10.0 1.0 1 1 1 1 -101.752816542 25891.5410156 10.1742255293 1 0.1 nan 1.0 1.0 1 0 0 0 -101.754218528 25756.6875 10.3110174589 1 0.1 nan 1.0 1.0 1 0 0 0 -101.754919587 25550.6679688 10.2443423925 1 0.1 nan 1.0 1.0 1 0 0 0 -101.756286448 28137.671875 11.0568551849 1 0.1 nan 1.0 1.0 1 0 0 0 -101.761808201 26206.2382812 10.5071882309 1 0.1 nan 1.0 1.0 1 0 0 0 -101.764257907 31043.203125 11.902539427 1 0.1 nan 1.0 1.0 1 0 0 0 -101.764709916 28157.2539062 10.7816060363 1 0.1 nan 1.0 1.0 1 0 0 0 -101.76604175 26935.96875 10.7815407996 1 0.1 nan 1.0 1.0 1 0 0 0 -101.773779191 32049.0517578 12.5003202925 2 0.2 30.3025137535 2.0 1.0 1 0 0 0 -101.774853717 29703.9023438 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--- a/test-data/batch04_S01_rep01_247_2_248_3_249.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/batch04_S01_rep01_247_2_248_3_249.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,238 +1,238 @@ mz intensity snr present fraction rsd occurrence purity intra_count flags -98.9954985809 75661.9152344 29.1450101692 3.0 1.0 3.24620218295 3.0 1.0 1.0 1 -104.106969562 29157.5138579 11.4029541309 2.0 0.666666666667 1.81090910662 2.0 1.0 1.0 1 -112.05230127 69397.7929688 26.6706097673 3.0 1.0 15.0331582108 3.0 1.0 1.0 1 -118.086254325 171352.920833 65.9129785479 3.0 1.0 7.45508041745 3.0 1.0 1.0 1 -123.013846528 33188.405136 12.8361207096 3.0 1.0 10.4918660185 3.0 1.0 1.0 1 -128.010842465 32625.4074508 12.5887141682 3.0 1.0 1.3096676284 3.0 1.0 1.0 1 -128.994852728 47105.5606771 18.1738870974 3.0 1.0 2.43755566223 3.0 1.0 1.0 1 -131.009840858 32450.8670573 12.5029416526 3.0 1.0 3.90521799017 3.0 1.0 1.0 1 -131.010519286 101834.059896 39.2420940643 3.0 1.0 2.31530284585 3.0 1.0 1.0 1 -131.018941789 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filelist_multilist_merge.txt Tue Apr 28 17:21:19 2020 -0400 @@ -0,0 +1,14 @@ +filename classLabel multilist +batch04_B02_rep01_301.mzML blank 1 +batch04_B02_rep02_302.mzML blank 2 +batch04_B02_rep03_303.mzML blank 3 +batch04_S01_rep01_247.mzML sample 1 +batch04_S01_rep02_248.mzML sample 2 +batch04_S01_rep03_249.mzML sample 3 +batch04_QC17_rep01_262.mzML QC 1 +batch04_QC17_rep02_263.mzML QC 2 +batch04_QC17_rep03_264.mzML QC 3 +batch04_QC18_rep01_280.mzML QC 1 +batch04_QC18_rep02_281.mzML QC 2 +batch04_QC18_rep03_282.mzML QC 3 +
--- a/test-data/peak_matrix_as.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,4 @@ -mz 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 128.994858336 129.090369007 129.090974735 129.127358602 130.049222294 130.049863468 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71786.90042162698 0.0 83165.90859375 22083.000054253473 44524.117838541664 53219.14762524801 563467.5061507936 61452.02628348215 121461.7700768849 0.0 22174.78709387401 234800.5678075397 37164.13912450397 45122.278782242065 434254.0575892857 0.0 37092.6867094494 0.0 0.0 0.0 25167.232475532277 33594.23033234127 24355.07425130208 163861.21207837304 23160.409028552825 21964.984381070317 45369.46999007937 42101.45017981151 105624.26633184524 22512.405451221955 63188.038981894846 0.0 52955.537586805556 25661.12863498264 0.0 22295.725614050665 28190.34890562996 0.0 186318.82165178572 45349.41780753967 28129.257837301586 52889.21351066468 37808.08317212301 29538.234872462606 48844.13542906746 96244.65724826389 43880.41099950397 0.0 0.0 574059.2974206349 57604.329699900794 78127.08833085316 29071.199028862848 42197.10287388393 41416.60560515873 0.0 110157.38332093252 35188.02998511904 36365.887481398815 133851.82312748017 1030898.4673611111 179443.6574404762 74687.60083085317 32620.488847036217 0.0 178877.27758699632 424581.2103670635 9470685.434920633 27564.084517045456 83400.00447668652 0.0 58153.763510664685 144474.41946924603 1424719.7924603175 0.0 44984.337617807534 475144.3658730159 108507.60205853176 83007.32730654762 83981.03370535716 34242.966317894345 29854.664903428824 0.0 0.0 29646.761100260417 118081.91984126985 32592.69900841346 86720.41920572917 0.0 152571.80000000002 87342.69348958334 0.0 0.0 33841.54955667162 33583.98621544471 30602.864388020833 51473.89185267858 0.0 0.0 21959.403428024525 34300.02285084707 29778.227435325087 0.0 67241.27692522321 146305.93179086538 101036.59263392858 21652.256227171267 32429.397868732824 0.0 32222.753627232145 175021.82620764652 38369.65066964286 0.0 0.0 0.0 0.0 22986.03489467076 40652.68815819597 125281.94421073717 333543.3009958791 88068.38630022321 32840.781529017855 142280.7689732143 26541.65380859375 42199.84211166437 78079.77403846155 0.0 108447.62866300368 0.0 26641.51653001946 24296.99882669414 17470.76630108173 22751.907934838597 0.0 26518.350986578527 40548.65718363667 19661.2511033888 18431.780284288194 18001.393269328328 18000.480342158564 0.0 46093.60970409799 69388.91271749085 40983.13309867216 32112.224584334937 24770.567856785143 22212.35483201694 19070.327774439105 154255.92180345696 0.0 1063613.3790064103 31026.94250606165 225684.52017513735 0.0 62285.55141082875 19884.966638035 17934.41134505685 19090.488504523906 19432.625684428418 19107.323294354297 0.0 0.0 25360.814503205125 203560.85456730766 60629.850661057695 29693.776392227563 26134.797225560895 19277.67814962273 23161.988882211543 40219.91942107372 0.0 29817.913211137817 32708.132211538457 84717.53425480769 27774.176382211535 18993.78022335737 0.0 24053.999774639422 24988.022135416668 16436.94230433873 22073.400265424683 20138.11379248464 0.0 46858.108849158656 17052.917613636364 21167.99749599359 34787.16932091346 23414.47551081731 37938.5930488782 19106.909016927082 0.0 21314.30626502404 71192.1812984108 20811.27083124666 15141.079609070941 0.0 0.0 15828.400472953695 0.0 14286.520396175547 0.0 0.0 24021.255167643227 717237.7735293135 321793.08984375 32279.772057166465 40430.64118214142 16052.60376602564 196613.67998798075 59718.0442290999 30108.734554453793 47967.01162997159 3177844.6084401705 102904.26472355769 0.0 110199.69451121795 15230.836681189903 22302.9383346688 988971.0830662394 0.0 231091.9709869124 121895.14788661858 59537.79195045406 24667.618235009348 18404.367871928418 74641.00673577725 23476.390441372863 14867.328322393752 37019.75827991453 34291.01029563969 16201.09990985577 392976.7027911325 107441.14918870192 34247.425743689906 \ No newline at end of file
--- a/test-data/peak_matrix_as_bf_compr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_compr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,10 +1,10 @@ -mz missing values tags_injectionOrder tags_classLabel tags_replicates tags_untyped 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 128.994858336 129.090369007 129.090974735 129.127358602 130.049222294 130.049863468 130.964513436 130.965138358 131.009836808 131.010517825 131.018942036 131.070233883 131.085482301 131.106615399 132.074583988 132.075008963 132.075567318 132.076101717 132.076671348 132.077202011 132.077992635 132.078371418 132.10124611 132.101899697 133.034572295 133.073124466 133.073801709 133.078935658 133.079460494 133.080118687 133.080632528 133.085244134 133.08588551 133.100506766 133.101138251 133.105278546 134.080996946 134.986830233 134.996465421 135.002862414 135.044024062 135.079258734 135.079764229 135.08038938 135.08097732 135.100884718 135.101532646 135.116137118 135.116787748 136.021508699 136.04691347 136.047429382 136.048119883 136.048697166 136.061765976 136.073251744 136.083096309 136.083761924 136.940051855 137.029491761 137.045065286 137.045773739 137.056596193 137.057269511 137.058997556 137.059672042 137.094876372 137.095391733 137.096043901 137.096633067 137.132444496 138.091309182 138.099413241 139.015603989 139.036530811 139.072917036 139.074630285 139.075322774 139.111014214 139.111701664 140.066921905 140.067478979 140.06819156 140.068751041 140.106954463 140.115061283 141.015855767 141.05218138 141.071577375 141.087852717 141.088567109 141.090252262 141.090971445 141.127355825 142.047430796 142.086228559 142.121881522 142.122604088 142.158992032 142.94808538 143.001525805 143.085493568 143.10588682 143.106624835 143.988083681 144.080733504 144.101942195 144.980789437 145.047092142 145.101135997 145.122261684 146.116764318 146.117593543 146.165212548 146.99644084 147.075026099 147.07563403 147.076381496 147.076979975 147.080407767 147.112840746 147.116791771 148.002470297 148.003082516 148.003895413 148.004529246 148.059020674 148.059628878 148.060463029 148.061104039 148.079812778 149.002478676 149.022503043 149.023281113 149.044827912 149.059672206 149.063819045 149.09606266 149.132443185 149.999720327 150.975955392 150.976840465 152.022107353 152.106952838 155.106635915 156.041293988 156.04209741 156.076741027 156.989754618 157.045485596 158.040247352 158.117532287 158.921989272 159.027720801 159.065165762 160.133198751 161.128432541 162.110690219 162.111590644 162.112377858 162.113089295 163.045136563 163.114854206 163.115822095 163.148118188 163.976056014 163.976865689 163.977780102 165.97362311 165.975937112 166.086251818 166.950728597 167.021727034 167.104235181 168.00575923 169.058369029 169.122302355 170.031627109 170.032608751 170.117542392 171.036000371 171.10155643 172.03075001 172.131391412 172.132189987 172.133058362 172.984687975 173.080840757 173.132465407 173.136536346 174.112454069 174.89594473 175.001680018 175.118963541 175.148114856 176.102979229 177.134608611 179.128465135 180.099485034 181.064781256 183.135542334 184.09440398 186.1488452 187.125928194 188.126027407 188.126982017 188.127958364 189.052399827 189.112130373 189.131443965 189.159733638 191.040098978 191.104244442 191.106642836 191.139020145 191.143026735 191.164168196 193.001987153 193.107326275 193.122293797 193.158657464 194.112909063 194.113937225 194.115013807 194.162041956 195.017597191 195.099164614 195.118489509 195.122688638 195.137953706 195.174329384 196.093111731 196.094365648 196.133188662 196.954419421 197.078436232 197.151198232 197.15359074 198.084934735 198.11005386 198.148826946 198.185230589 199.094085221 199.130443878 199.13285878 199.167928041 199.169182065 199.20565281 200.067015416 200.068336832 200.128114646 200.163168249 200.164421525 200.172596426 200.200872992 201.071723083 201.112137504 201.148516239 201.167861307 201.18489544 201.932346714 201.933718688 202.066511789 202.143739474 202.180178742 203.040079527 203.051224356 203.052583123 203.139034837 203.931844481 204.04214677 204.056007584 204.120741567 204.121476777 204.122881675 204.123967408 205.055741463 205.08591946 205.097182566 205.122293634 205.124995123 205.126369088 205.154711374 205.158691684 205.195062356 206.05531063 206.1273128 207.014274578 207.078225213 207.101570295 207.137952093 207.159083317 207.174339207 207.988550264 207.998291404 208.09441105 208.130805683 208.169561137 209.117232919 209.153584829 209.172945534 209.177406022 209.189980267 210.087340882 210.089121447 210.107509217 210.109927964 210.148859874 210.156956315 210.185237724 210.940588306 210.970069553 210.985281317 211.094097176 211.096498226 211.113409698 211.169225897 212.125679781 212.128118487 212.1644968 213.0671985 213.146104172 213.568883933 214.058850666 214.089621826 214.101814932 214.143778719 214.1801328 214.25290771 215.069634252 215.104251358 215.16417564 216.159420321 217.104653094 217.10704668 217.195075119 218.137147136 218.138617868 218.18633146 219.017655316 219.026587805 219.142081286 219.174338426 220.130795435 222.029254451 222.072488512 222.11007085 222.146462571 222.988227171 224.125710227 226.104758587 226.141172094 226.216351729 227.113639423 228.195607363 228.231982987 229.152780695 229.154420238 229.235339774 230.157792453 231.144938826 232.151182802 232.152363977 232.154032856 232.155655558 233.157441453 235.066006489 236.112634358 236.992211984 238.022752298 240.156763779 241.068017602 241.129235983 241.154393751 242.078631865 242.115014467 242.211210704 242.247584644 243.122455564 243.210475071 244.188471352 244.190460473 245.13541974 245.147333125 245.149278063 245.193820273 245.226122415 246.152668181 246.169719791 246.180951474 246.229471008 247.239723356 247.241744513 248.146977998 248.148957043 248.245104092 249.045257364 249.153279612 249.155411959 249.157303366 250.158796263 250.213863329 252.231933281 253.094618769 254.018746292 254.136012391 254.172397297 254.247550244 255.13541146 255.25092891 256.085360003 256.261072254 256.263172006 257.041913238 257.091126293 257.266565794 258.109821983 260.149011786 260.185330942 260.196578012 261.188683931 261.221025953 262.128218019 262.164606458 262.224398625 263.145935141 263.234440169 263.236655987 264.172129098 264.229520712 264.240028783 265.104355337 265.250033729 265.252253428 266.17238731 266.187766715 266.25563392 267.11025096 268.226814282 268.263184289 269.087730151 270.109886656 270.242478486 270.278821805 271.137356381 271.282204136 273.005664599 274.273747968 275.200258608 276.180208183 276.229452113 277.215910977 278.245106853 278.24743694 279.231549941 279.24849795 280.091705372 280.234931872 280.263159033 282.276314566 282.278771803 283.282149772 284.294439776 285.297819224 292.203326231 292.22461117 292.226693455 292.260726845 293.071380726 293.206676616 294.242397854 296.06590552 296.255309681 296.258064538 297.261519018 298.273784757 298.992809793 299.277185934 299.305464022 302.242399929 302.245285265 303.24878925 304.255907829 304.260692167 304.263413947 304.284326598 305.264271955 306.21928064 306.240073417 306.267667028 306.27646577 307.038665497 307.040712241 307.043708382 307.24345132 308.047169681 308.090980265 308.219394644 308.235022494 309.041951809 310.046940741 310.23737757 310.310188233 311.240728759 312.253038734 312.325779705 313.947170267 314.268692583 316.203654392 316.284338019 316.320838619 317.114880954 318.213669955 318.215940621 318.219163989 318.236907034 318.240142545 319.222645274 319.243424326 319.25884422 320.217490758 320.224871533 320.227902206 320.229134825 320.231111598 320.234511416 320.241626804 320.252365774 320.255652339 320.974705507 321.201833228 321.232197081 321.234813105 321.238113065 321.259056543 321.892351677 322.229522709 322.23301528 322.241621481 322.250574378 323.225432289 323.236408988 324.214242464 326.948386194 327.007825925 328.067170959 328.247935186 329.004857836 330.072826092 330.263572292 330.299955743 331.039968776 331.295183719 332.028813361 332.219286575 332.279199398 333.222664444 334.214166454 334.234903638 334.250668262 334.271616498 335.21743312 335.238292815 336.229835303 336.250584667 336.948656669 337.253933854 338.266234235 338.341538219 338.985191711 339.34477402 340.188249498 340.357043677 346.046894367 348.070300004 348.214239665 348.266379527 350.22981425 350.25403947 351.233219733 352.224602434 352.245328978 352.281804984 353.248853115 355.069613759 357.249414386 360.323388318 361.326682865 366.203861182 366.224939197 366.231260276 367.228325785 367.234706465 368.219424431 368.24046607 369.222872079 369.231029221 369.243877534 370.052089279 370.217696745 370.247962938 371.100992983 371.326530086 372.206249404 372.245046935 372.329856912 373.244333087 374.203335574 375.248668175 376.232769254 376.29721222 377.300668857 378.295467348 378.31301879 379.151332229 379.220085516 380.210574659 380.276854028 381.079072477 381.235717465 382.219859851 382.226201653 383.11569564 384.206323385 384.235382908 385.316989323 386.025883713 386.221824198 386.326137763 387.175389856 387.17979564 387.225262028 387.329555386 387.332638188 388.183221797 388.218983046 389.222358733 389.337051636 391.283986477 392.313138217 393.358426888 394.27986697 395.125200243 395.33770243 396.25078971 396.308075518 396.341053427 397.230555757 398.020297889 398.032874064 398.214626213 398.221077356 399.144242079 399.357767697 400.157233205 404.206390978 405.209768165 407.293469086 408.007909317 408.020525014 408.307997616 408.951037638 409.056820106 409.150397774 409.161689196 409.165861619 409.311424341 410.165154057 411.168907239 411.332645717 413.348315017 413.373403903 414.006828619 414.215973762 415.156897262 416.084309262 423.981765103 424.281826443 425.125683491 425.135463252 425.28532915 426.138910614 426.280170349 427.133904681 427.142968192 429.088364033 429.262746682 435.061172652 435.330083765 435.988638501 437.138585394 443.081997167 443.233520419 445.119543726 445.249096557 445.988977013 446.252850916 448.375554388 450.329735454 451.962532082 453.068896429 453.112608304 453.368281035 453.404538988 454.040051872 456.273048614 457.043005407 461.332821274 461.334313821 461.962854671 465.365351627 467.23109072 467.383807279 468.387109722 469.055315064 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1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 -rsd_all nan nan nan nan 7.44464804268 nan nan nan nan nan nan nan nan nan nan 7.95741393603 nan nan nan nan nan nan nan nan nan 48.9403897991 nan nan nan 16.1208244867 nan nan nan nan nan nan nan nan nan 40.0877914687 nan nan nan nan nan 7.42140723217 nan nan nan nan nan nan nan 19.0959428766 4.02320389621 nan nan nan nan 69.0168382411 nan nan 1.97751570629 16.520015012 2.31482831144 nan nan nan 21.6810898698 23.7716957344 22.6647952447 19.8082794922 19.450155988 20.9925495033 18.2702430845 nan 2.72928869643 83.8750434369 66.1115208021 15.9195461534 12.327067359 11.4879595591 16.6762667568 18.4675195476 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--- a/test-data/peak_matrix_as_bf_sf_compr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_compr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,11 +1,11 @@ -mz missing values tags_classLabel tags_untyped 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 128.994858336 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311.240728759 312.253038734 312.325779705 313.947170267 314.268692583 316.203654392 316.284338019 316.320838619 317.114880954 318.213669955 318.215940621 318.219163989 318.236907034 318.240142545 319.222645274 319.243424326 319.25884422 320.217490758 320.224871533 320.227902206 320.229134825 320.231111598 320.234511416 320.241626804 320.252365774 320.255652339 320.974705507 321.201833228 321.232197081 321.234813105 321.238113065 321.259056543 321.892351677 322.229522709 322.23301528 322.241621481 322.250574378 323.225432289 323.236408988 324.214242464 326.948386194 327.007825925 328.067170959 328.247935186 329.004857836 330.072826092 330.263572292 330.299955743 331.039968776 331.295183719 332.028813361 332.219286575 332.279199398 333.222664444 334.214166454 334.234903638 334.250668262 334.271616498 335.21743312 335.238292815 336.229835303 336.250584667 336.948656669 337.253933854 338.266234235 338.341538219 338.985191711 339.34477402 340.188249498 340.357043677 346.046894367 348.070300004 348.214239665 348.266379527 350.22981425 350.25403947 351.233219733 352.224602434 352.245328978 352.281804984 353.248853115 355.069613759 357.249414386 360.323388318 361.326682865 366.203861182 366.224939197 366.231260276 367.228325785 367.234706465 368.219424431 368.24046607 369.222872079 369.231029221 369.243877534 370.052089279 370.217696745 370.247962938 371.100992983 371.326530086 372.206249404 372.245046935 372.329856912 373.244333087 374.203335574 375.248668175 376.232769254 376.29721222 377.300668857 378.295467348 378.31301879 379.151332229 379.220085516 380.210574659 380.276854028 381.079072477 381.235717465 382.219859851 382.226201653 383.11569564 384.206323385 384.235382908 385.316989323 386.025883713 386.221824198 386.326137763 387.175389856 387.17979564 387.225262028 387.329555386 387.332638188 388.183221797 388.218983046 389.222358733 389.337051636 391.283986477 392.313138217 393.358426888 394.27986697 395.125200243 395.33770243 396.25078971 396.308075518 396.341053427 397.230555757 398.020297889 398.032874064 398.214626213 398.221077356 399.144242079 399.357767697 400.157233205 404.206390978 405.209768165 407.293469086 408.007909317 408.020525014 408.307997616 408.951037638 409.056820106 409.150397774 409.161689196 409.165861619 409.311424341 410.165154057 411.168907239 411.332645717 413.348315017 413.373403903 414.006828619 414.215973762 415.156897262 416.084309262 423.981765103 424.281826443 425.125683491 425.135463252 425.28532915 426.138910614 426.280170349 427.133904681 427.142968192 429.088364033 429.262746682 435.061172652 435.330083765 435.988638501 437.138585394 443.081997167 443.233520419 445.119543726 445.249096557 445.988977013 446.252850916 448.375554388 450.329735454 451.962532082 453.068896429 453.112608304 453.368281035 453.404538988 454.040051872 456.273048614 457.043005407 461.332821274 461.334313821 461.962854671 465.365351627 467.23109072 467.383807279 468.387109722 469.055315064 469.324281969 469.399446217 469.410689679 470.013893312 470.269457183 471.061108818 471.132585306 471.378710779 472.135479775 473.01699606 473.39436478 475.350033618 475.386377616 476.227406838 476.332575866 477.365665277 479.335260946 479.344745681 481.363458943 483.017348311 483.075340494 483.378625136 483.944790467 484.311374779 484.323934317 485.394293013 487.373634744 489.226592154 489.365575861 490.368969715 491.344991495 491.38122824 493.360516009 499.918623596 500.238489651 503.344870637 503.38120115 507.377444117 515.395294096 515.412843212 516.401798594 516.408840124 516.416514227 517.385592616 517.396406557 517.409456211 517.420223387 518.25000135 518.412653011 519.253359366 519.295091303 521.356742234 521.393036958 523.35110107 523.372346256 523.408704507 524.37571877 525.351630414 525.387723492 527.183398853 531.408077733 532.395950104 532.411787242 532.423350278 532.430260266 532.439566555 533.249780822 533.443291391 535.372514295 535.520217732 537.378385302 537.394161094 537.535700424 538.381964514 538.398104966 538.406404199 538.539157819 539.367636975 539.39113038 539.401854296 540.394709222 541.361719514 542.215451048 545.40662442 545.423300216 546.426817562 547.419387343 547.430522439 547.460189893 548.28553146 549.289149666 549.38814471 550.360250738 553.348831297 553.367591025 553.369576087 553.376240677 553.386107823 553.388587287 553.390474419 554.278572222 554.355151822 554.371473263 554.372878572 554.393408035 555.355223456 555.366527064 555.37434307 555.398630939 556.370112699 556.40232674 557.073628299 557.095013624 557.501974295 558.505341074 559.151213812 559.517386251 561.535808365 563.551455252 564.554937793 569.345464898 569.363651248 570.367404206 571.361841884 -present 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 3 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 3 1 1 2 2 2 1 1 1 2 2 2 2 2 2 2 1 2 3 3 2 2 2 2 2 2 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 3 2 2 1 1 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 2 2 2 1 1 2 1 2 2 2 2 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 2 2 1 1 1 1 1 1 1 2 2 2 1 3 2 2 2 2 1 1 2 2 1 2 2 2 2 1 2 2 1 2 2 1 1 1 2 1 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 2 2 3 2 1 2 1 2 3 2 2 1 1 1 2 2 1 1 1 2 2 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 2 1 1 2 1 1 1 2 1 1 1 1 2 1 1 2 2 1 2 1 2 2 2 1 2 2 1 1 2 1 1 2 1 2 2 1 1 1 1 1 2 2 2 2 1 1 2 2 1 1 1 3 2 2 3 2 2 2 1 2 3 1 1 1 1 1 3 1 1 1 1 3 2 1 1 2 1 2 2 1 1 2 2 1 2 1 3 1 1 1 1 2 3 1 2 3 1 1 2 2 2 1 3 1 1 1 1 1 2 3 1 3 1 1 1 1 1 2 2 3 2 2 1 1 1 1 2 2 1 1 2 1 1 1 1 2 1 1 1 3 1 2 3 1 2 3 2 1 2 1 1 1 2 1 2 2 1 1 2 2 1 1 1 1 1 1 1 2 1 3 2 1 2 2 1 3 2 1 1 2 1 1 1 1 2 1 1 3 2 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 2 2 2 1 1 3 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 3 1 2 1 1 2 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 1 3 1 1 1 3 1 2 2 1 1 2 1 1 1 2 2 1 2 1 3 2 2 1 2 2 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 2 1 1 2 1 2 2 1 2 1 1 1 1 1 1 1 2 2 1 1 3 1 1 1 1 1 1 2 1 1 1 1 1 1 2 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 3 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 3 2 1 1 2 3 3 2 1 3 1 1 1 3 3 1 1 1 1 2 2 1 1 1 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 2 1 2 2 1 2 1 1 2 1 1 2 1 1 3 2 1 2 2 1 -occurrence 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 2.0 3.0 3.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 3.0 2.0 1.0 2.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 3.0 2.0 2.0 3.0 2.0 2.0 2.0 1.0 2.0 3.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 2.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 2.0 3.0 1.0 2.0 3.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 3.0 2.0 1.0 2.0 2.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 3.0 1.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 3.0 1.0 1.0 1.0 3.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 3.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 3.0 3.0 2.0 1.0 3.0 1.0 1.0 1.0 3.0 3.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 2.0 1.0 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--- a/test-data/peak_matrix_as_bf_sf_mv.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_mv.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,3 +1,3 @@ -mz 98.9954998691 104.106972509 112.052301283 118.086253653 123.013845316 128.010843476 128.994858336 131.009836808 131.010517825 131.018942036 132.074583988 132.075008963 132.075567318 132.076101717 132.076671348 132.077202011 132.077992635 132.10124611 132.101916959 133.073124466 133.073801709 133.078935658 133.079460494 133.080118687 133.080632528 134.080996946 135.002862414 136.047429382 136.04813128 136.048697166 136.061765976 136.940051855 137.029491761 137.045781605 139.015603989 140.066921905 140.067478979 140.06819156 144.101942195 146.116764318 146.117593543 146.165212548 147.075026099 147.07563403 147.076381496 147.112840746 148.002470297 148.003082516 148.003895413 148.004529246 148.059628878 148.060463029 148.061104039 148.079812778 150.976840465 152.022107353 156.041293988 156.04209741 156.076741027 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--- a/test-data/peak_matrix_as_bf_sf_mz.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_mz.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,238 +1,238 @@ mz batch04_B02_rep01_301_2_302_3_303 batch04_QC17_rep01_262_2_263_3_264 batch04_S01_rep01_247_2_248_3_249 -98.9954998691 0.0 98.9955011572 98.9954985809 -104.106972509 0.0 104.106975455 104.106969562 -112.052301283 0.0 112.052301296 112.05230127 -118.086253653 0.0 118.086252982 118.086254325 -123.013845316 0.0 123.013844104 123.013846528 -128.010843476 0.0 128.010844488 128.010842465 -128.994858336 0.0 128.994863945 128.994852728 -131.009836808 0.0 131.009832759 131.009840858 -131.010517825 0.0 131.010516364 131.010519286 -131.018942036 0.0 131.018942282 131.018941789 -132.074583988 0.0 132.074579642 132.074588333 -132.075008963 0.0 132.075002532 132.075015393 -132.075567318 0.0 132.075557576 132.075577059 -132.076101717 0.0 132.076094335 132.076109099 -132.076671348 0.0 132.076676827 132.07666587 -132.077202011 0.0 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No newline at end of file
--- a/test-data/peak_matrix_as_bf_sf_mz_compr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_mz_compr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,897 +1,899 @@ mz present occurrence purity rsd_all blank_flag fraction_flag flags batch04_B02_rep01_301_2_302_3_303 batch04_QC17_rep01_262_2_263_3_264 batch04_S01_rep01_247_2_248_3_249 missing values 231 0 0 tags_classLabel blank QC sample +tags_injectionOrder 1 4 7 +tags_replicates 1-2-3 1-2-3 1-2-3 tags_untyped -95.0854867136 1 1.0 1.0 nan 0 0 0 95.0854867136 0.0 0.0 -96.0477230462 1 1.0 1.0 nan 0 0 0 96.0477230462 0.0 0.0 -97.0647529114 1 1.0 1.0 nan 0 0 0 97.0647529114 0.0 0.0 -97.1011384065 1 1.0 1.0 nan 0 0 0 97.1011384065 0.0 0.0 -98.9954998691 2 2.0 1.0 7.44464804268 1 1 1 0.0 98.9955011572 98.9954985809 -99.0804011767 1 1.0 1.0 nan 0 0 0 99.0804011767 0.0 0.0 -101.003118017 1 1.0 1.0 nan 0 0 0 101.003118017 0.0 0.0 -101.059284262 1 1.0 1.0 nan 0 0 0 101.059284262 0.0 0.0 -101.059667337 1 1.0 1.0 nan 0 0 0 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--- a/test-data/peak_matrix_as_bf_sf_within.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_within.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,4 @@ -mz 98.9954998691 101.777300408 101.781524007 103.038951206 104.106972509 112.052301283 115.036557299 116.070599012 118.086253653 123.013845316 123.055288913 126.021940468 128.010843476 128.994858336 130.049222294 131.009836808 131.010517825 131.018942036 132.074583988 132.075008963 132.075567318 132.076101717 132.076671348 132.077202011 132.077992635 132.078371418 132.10124611 132.101899697 133.073124466 133.073801709 133.078935658 133.079460494 133.080118687 133.080632528 133.105278546 134.080996946 135.002862414 136.04691347 136.047429382 136.048119883 136.048697166 136.061765976 136.940051855 137.029491761 137.045065286 137.045773739 139.015603989 140.066921905 140.067478979 140.06819156 140.068751041 141.015855767 141.071577375 142.94808538 143.988083681 144.101942195 146.116764318 146.117593543 146.165212548 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--- a/test-data/peak_matrix_as_bf_sf_within_compr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_bf_sf_within_compr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,11 +1,11 @@ -mz missing values tags_classLabel tags_untyped 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 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469.399446217 469.410689679 470.013893312 470.269457183 471.061108818 471.132585306 471.378710779 472.135479775 473.01699606 473.39436478 475.350033618 475.386377616 476.227406838 476.332575866 477.365665277 479.335260946 479.344745681 481.363458943 483.017348311 483.075340494 483.378625136 483.944790467 484.311374779 484.323934317 485.394293013 487.373634744 489.226592154 489.365575861 490.368969715 491.344991495 491.38122824 493.360516009 499.918623596 500.238489651 503.344870637 503.38120115 507.377444117 515.395294096 515.412843212 516.401798594 516.408840124 516.416514227 517.385592616 517.396406557 517.409456211 517.420223387 518.25000135 518.412653011 519.253359366 519.295091303 521.356742234 521.393036958 523.35110107 523.372346256 523.408704507 524.37571877 525.351630414 525.387723492 527.183398853 531.408077733 532.395950104 532.411787242 532.423350278 532.430260266 532.439566555 533.249780822 533.443291391 535.372514295 535.520217732 537.378385302 537.394161094 537.535700424 538.381964514 538.398104966 538.406404199 538.539157819 539.367636975 539.39113038 539.401854296 540.394709222 541.361719514 542.215451048 545.40662442 545.423300216 546.426817562 547.419387343 547.430522439 547.460189893 548.28553146 549.289149666 549.38814471 550.360250738 553.348831297 553.367591025 553.369576087 553.376240677 553.386107823 553.388587287 553.390474419 554.278572222 554.355151822 554.371473263 554.372878572 554.393408035 555.355223456 555.366527064 555.37434307 555.398630939 556.370112699 556.40232674 557.073628299 557.095013624 557.501974295 558.505341074 559.151213812 559.517386251 561.535808365 563.551455252 564.554937793 569.345464898 569.363651248 570.367404206 571.361841884 -present 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 3 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 3 1 1 2 2 2 1 1 1 2 2 2 2 2 2 2 1 2 3 3 2 2 2 2 2 2 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 3 2 2 1 1 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 2 2 2 1 1 2 1 2 2 2 2 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 2 2 1 1 1 1 1 1 1 2 2 2 1 3 2 2 2 2 1 1 2 2 1 2 2 2 2 1 2 2 1 2 2 1 1 1 2 1 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 2 2 3 2 1 2 1 2 3 2 2 1 1 1 2 2 1 1 1 2 2 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 2 1 1 2 1 1 1 2 1 1 1 1 2 1 1 2 2 1 2 1 2 2 2 1 2 2 1 1 2 1 1 2 1 2 2 1 1 1 1 1 2 2 2 2 1 1 2 2 1 1 1 3 2 2 3 2 2 2 1 2 3 1 1 1 1 1 3 1 1 1 1 3 2 1 1 2 1 2 2 1 1 2 2 1 2 1 3 1 1 1 1 2 3 1 2 3 1 1 2 2 2 1 3 1 1 1 1 1 2 3 1 3 1 1 1 1 1 2 2 3 2 2 1 1 1 1 2 2 1 1 2 1 1 1 1 2 1 1 1 3 1 2 3 1 2 3 2 1 2 1 1 1 2 1 2 2 1 1 2 2 1 1 1 1 1 1 1 2 1 3 2 1 2 2 1 3 2 1 1 2 1 1 1 1 2 1 1 3 2 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 2 2 2 1 1 3 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 3 1 2 1 1 2 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 1 3 1 1 1 3 1 2 2 1 1 2 1 1 1 2 2 1 2 1 3 2 2 1 2 2 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 2 1 1 2 1 2 2 1 2 1 1 1 1 1 1 1 2 2 1 1 3 1 1 1 1 1 1 2 1 1 1 1 1 1 2 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 3 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 3 2 1 1 2 3 3 2 1 3 1 1 1 3 3 1 1 1 1 2 2 1 1 1 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 2 1 2 2 1 2 1 1 2 1 1 2 1 1 3 2 1 2 2 1 -occurrence 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 2.0 3.0 3.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 3.0 2.0 1.0 2.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 3.0 2.0 2.0 3.0 2.0 2.0 2.0 1.0 2.0 3.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 2.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 2.0 3.0 1.0 2.0 3.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 3.0 2.0 1.0 2.0 2.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 3.0 1.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 3.0 1.0 1.0 1.0 3.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 3.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 3.0 3.0 2.0 1.0 3.0 1.0 1.0 1.0 3.0 3.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 2.0 1.0 2.0 2.0 1.0 2.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 1.0 3.0 2.0 1.0 2.0 2.0 1.0 -purity 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 -rsd_all nan nan nan nan 7.44464804268 nan nan nan nan nan nan nan nan nan nan 7.95741393603 nan nan nan nan nan nan nan nan nan 48.9403897991 nan nan nan 16.1208244867 nan nan nan nan nan nan nan nan nan 40.0877914687 nan nan nan nan nan 7.42140723217 nan nan nan nan nan nan nan 19.0959428766 4.02320389621 nan nan nan nan 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--- a/test-data/peak_matrix_as_mz.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_mz.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,4 @@ -mz 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 128.994858336 129.090369007 129.090974735 129.127358602 130.049222294 130.049863468 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--- a/test-data/peak_matrix_as_mz_compr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_as_mz_compr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,9 +1,9 @@ -mz missing values tags_injectionOrder tags_classLabel tags_replicates tags_untyped 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 128.010843476 128.994858336 129.090369007 129.090974735 129.127358602 130.049222294 130.049863468 130.964513436 130.965138358 131.009836808 131.010517825 131.018942036 131.070233883 131.085482301 131.106615399 132.074583988 132.075008963 132.075567318 132.076101717 132.076671348 132.077202011 132.077992635 132.078371418 132.10124611 132.101899697 133.034572295 133.073124466 133.073801709 133.078935658 133.079460494 133.080118687 133.080632528 133.085244134 133.08588551 133.100506766 133.101138251 133.105278546 134.080996946 134.986830233 134.996465421 135.002862414 135.044024062 135.079258734 135.079764229 135.08038938 135.08097732 135.100884718 135.101532646 135.116137118 135.116787748 136.021508699 136.04691347 136.047429382 136.048119883 136.048697166 136.061765976 136.073251744 136.083096309 136.083761924 136.940051855 137.029491761 137.045065286 137.045773739 137.056596193 137.057269511 137.058997556 137.059672042 137.094876372 137.095391733 137.096043901 137.096633067 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--- a/test-data/peak_matrix_hdf5_to_txt_comprehensive_snr.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_hdf5_to_txt_comprehensive_snr.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,11 +1,11 @@ -mz missing values tags_classLabel tags_untyped 95.0854867136 96.0477230462 97.0647529114 97.1011384065 98.9954998691 99.0804011767 101.003118017 101.059284262 101.059667337 101.777300408 101.781524007 102.127686063 102.970223555 103.038951206 103.075318834 104.106972509 105.003234195 105.090964311 107.070230246 107.085062328 107.085488315 109.100703053 109.101137314 111.08040236 111.116786045 112.052301283 113.059666808 113.096051485 114.065677969 114.066170487 114.091302909 115.036557299 115.075318293 115.111705216 116.070599012 116.985382141 116.98587154 117.054583395 117.090968646 118.086253653 119.085485311 120.980267261 120.980786531 121.00756219 121.064754009 123.013845316 123.055288913 123.116788199 125.095487802 125.096051948 126.021940468 127.075321735 127.111706998 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264.229520712 264.240028783 265.104355337 265.250033729 265.252253428 266.17238731 266.187766715 266.25563392 267.11025096 268.226814282 268.263184289 269.087730151 270.109886656 270.242478486 270.278821805 271.137356381 271.282204136 273.005664599 274.273747968 275.200258608 276.180208183 276.229452113 277.215910977 278.245106853 278.24743694 279.231549941 279.24849795 280.091705372 280.234931872 280.263159033 282.276314566 282.278771803 283.282149772 284.294439776 285.297819224 292.203326231 292.22461117 292.226693455 292.260726845 293.071380726 293.206676616 294.242397854 296.06590552 296.255309681 296.258064538 297.261519018 298.273784757 298.992809793 299.277185934 299.305464022 302.242399929 302.245285265 303.24878925 304.255907829 304.260692167 304.263413947 304.284326598 305.264271955 306.21928064 306.240073417 306.267667028 306.27646577 307.038665497 307.040712241 307.043708382 307.24345132 308.047169681 308.090980265 308.219394644 308.235022494 309.041951809 310.046940741 310.23737757 310.310188233 311.240728759 312.253038734 312.325779705 313.947170267 314.268692583 316.203654392 316.284338019 316.320838619 317.114880954 318.213669955 318.215940621 318.219163989 318.236907034 318.240142545 319.222645274 319.243424326 319.25884422 320.217490758 320.224871533 320.227902206 320.229134825 320.231111598 320.234511416 320.241626804 320.252365774 320.255652339 320.974705507 321.201833228 321.232197081 321.234813105 321.238113065 321.259056543 321.892351677 322.229522709 322.23301528 322.241621481 322.250574378 323.225432289 323.236408988 324.214242464 326.948386194 327.007825925 328.067170959 328.247935186 329.004857836 330.072826092 330.263572292 330.299955743 331.039968776 331.295183719 332.028813361 332.219286575 332.279199398 333.222664444 334.214166454 334.234903638 334.250668262 334.271616498 335.21743312 335.238292815 336.229835303 336.250584667 336.948656669 337.253933854 338.266234235 338.341538219 338.985191711 339.34477402 340.188249498 340.357043677 346.046894367 348.070300004 348.214239665 348.266379527 350.22981425 350.25403947 351.233219733 352.224602434 352.245328978 352.281804984 353.248853115 355.069613759 357.249414386 360.323388318 361.326682865 366.203861182 366.224939197 366.231260276 367.228325785 367.234706465 368.219424431 368.24046607 369.222872079 369.231029221 369.243877534 370.052089279 370.217696745 370.247962938 371.100992983 371.326530086 372.206249404 372.245046935 372.329856912 373.244333087 374.203335574 375.248668175 376.232769254 376.29721222 377.300668857 378.295467348 378.31301879 379.151332229 379.220085516 380.210574659 380.276854028 381.079072477 381.235717465 382.219859851 382.226201653 383.11569564 384.206323385 384.235382908 385.316989323 386.025883713 386.221824198 386.326137763 387.175389856 387.17979564 387.225262028 387.329555386 387.332638188 388.183221797 388.218983046 389.222358733 389.337051636 391.283986477 392.313138217 393.358426888 394.27986697 395.125200243 395.33770243 396.25078971 396.308075518 396.341053427 397.230555757 398.020297889 398.032874064 398.214626213 398.221077356 399.144242079 399.357767697 400.157233205 404.206390978 405.209768165 407.293469086 408.007909317 408.020525014 408.307997616 408.951037638 409.056820106 409.150397774 409.161689196 409.165861619 409.311424341 410.165154057 411.168907239 411.332645717 413.348315017 413.373403903 414.006828619 414.215973762 415.156897262 416.084309262 423.981765103 424.281826443 425.125683491 425.135463252 425.28532915 426.138910614 426.280170349 427.133904681 427.142968192 429.088364033 429.262746682 435.061172652 435.330083765 435.988638501 437.138585394 443.081997167 443.233520419 445.119543726 445.249096557 445.988977013 446.252850916 448.375554388 450.329735454 451.962532082 453.068896429 453.112608304 453.368281035 453.404538988 454.040051872 456.273048614 457.043005407 461.332821274 461.334313821 461.962854671 465.365351627 467.23109072 467.383807279 468.387109722 469.055315064 469.324281969 469.399446217 469.410689679 470.013893312 470.269457183 471.061108818 471.132585306 471.378710779 472.135479775 473.01699606 473.39436478 475.350033618 475.386377616 476.227406838 476.332575866 477.365665277 479.335260946 479.344745681 481.363458943 483.017348311 483.075340494 483.378625136 483.944790467 484.311374779 484.323934317 485.394293013 487.373634744 489.226592154 489.365575861 490.368969715 491.344991495 491.38122824 493.360516009 499.918623596 500.238489651 503.344870637 503.38120115 507.377444117 515.395294096 515.412843212 516.401798594 516.408840124 516.416514227 517.385592616 517.396406557 517.409456211 517.420223387 518.25000135 518.412653011 519.253359366 519.295091303 521.356742234 521.393036958 523.35110107 523.372346256 523.408704507 524.37571877 525.351630414 525.387723492 527.183398853 531.408077733 532.395950104 532.411787242 532.423350278 532.430260266 532.439566555 533.249780822 533.443291391 535.372514295 535.520217732 537.378385302 537.394161094 537.535700424 538.381964514 538.398104966 538.406404199 538.539157819 539.367636975 539.39113038 539.401854296 540.394709222 541.361719514 542.215451048 545.40662442 545.423300216 546.426817562 547.419387343 547.430522439 547.460189893 548.28553146 549.289149666 549.38814471 550.360250738 553.348831297 553.367591025 553.369576087 553.376240677 553.386107823 553.388587287 553.390474419 554.278572222 554.355151822 554.371473263 554.372878572 554.393408035 555.355223456 555.366527064 555.37434307 555.398630939 556.370112699 556.40232674 557.073628299 557.095013624 557.501974295 558.505341074 559.151213812 559.517386251 561.535808365 563.551455252 564.554937793 569.345464898 569.363651248 570.367404206 571.361841884 -present 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 3 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 3 1 1 2 2 2 1 1 1 2 2 2 2 2 2 2 1 2 3 3 2 2 2 2 2 2 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 3 2 2 1 1 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 2 2 2 1 1 2 1 2 2 2 2 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 2 2 1 1 1 1 1 1 1 2 2 2 1 3 2 2 2 2 1 1 2 2 1 2 2 2 2 1 2 2 1 2 2 1 1 1 2 1 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 2 2 3 2 1 2 1 2 3 2 2 1 1 1 2 2 1 1 1 2 2 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 2 1 1 2 1 1 1 2 1 1 1 1 2 1 1 2 2 1 2 1 2 2 2 1 2 2 1 1 2 1 1 2 1 2 2 1 1 1 1 1 2 2 2 2 1 1 2 2 1 1 1 3 2 2 3 2 2 2 1 2 3 1 1 1 1 1 3 1 1 1 1 3 2 1 1 2 1 2 2 1 1 2 2 1 2 1 3 1 1 1 1 2 3 1 2 3 1 1 2 2 2 1 3 1 1 1 1 1 2 3 1 3 1 1 1 1 1 2 2 3 2 2 1 1 1 1 2 2 1 1 2 1 1 1 1 2 1 1 1 3 1 2 3 1 2 3 2 1 2 1 1 1 2 1 2 2 1 1 2 2 1 1 1 1 1 1 1 2 1 3 2 1 2 2 1 3 2 1 1 2 1 1 1 1 2 1 1 3 2 1 1 2 2 1 1 1 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 2 2 2 1 1 3 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 3 1 2 1 1 2 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 1 3 1 1 1 3 1 2 2 1 1 2 1 1 1 2 2 1 2 1 3 2 2 1 2 2 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 2 1 1 2 1 2 2 1 2 1 1 1 1 1 1 1 2 2 1 1 3 1 1 1 1 1 1 2 1 1 1 1 1 1 2 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 3 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 3 2 1 1 2 3 3 2 1 3 1 1 1 3 3 1 1 1 1 2 2 1 1 1 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 2 1 2 2 1 2 1 1 2 1 1 2 1 1 3 2 1 2 2 1 -occurrence 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 2.0 3.0 3.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 2.0 2.0 2.0 2.0 3.0 2.0 1.0 2.0 1.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 2.0 2.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 3.0 2.0 2.0 3.0 2.0 2.0 2.0 1.0 2.0 3.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 2.0 3.0 1.0 1.0 2.0 2.0 2.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 3.0 1.0 3.0 1.0 1.0 1.0 1.0 1.0 2.0 2.0 3.0 2.0 2.0 1.0 1.0 1.0 1.0 2.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 3.0 1.0 2.0 3.0 1.0 2.0 3.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 2.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 3.0 2.0 1.0 2.0 2.0 1.0 3.0 2.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 3.0 2.0 1.0 1.0 2.0 2.0 1.0 1.0 1.0 2.0 2.0 2.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 2.0 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--- a/test-data/peak_matrix_hdf5_to_txt_intensity.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/peak_matrix_hdf5_to_txt_intensity.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,897 +1,899 @@ mz present occurrence purity rsd_all blank_flag fraction_flag flags batch04_B02_rep01_301_2_302_3_303 batch04_QC17_rep01_262_2_263_3_264 batch04_S01_rep01_247_2_248_3_249 missing values 231 0 0 tags_classLabel blank QC sample +tags_injectionOrder 1 4 7 +tags_replicates 1-2-3 1-2-3 1-2-3 tags_untyped -95.0854867136 1 1.0 1.0 nan 0 0 0 8190.6069987 0.0 0.0 -96.0477230462 1 1.0 1.0 nan 0 0 0 5827.43671203 0.0 0.0 -97.0647529114 1 1.0 1.0 nan 0 0 0 5479.02718099 0.0 0.0 -97.1011384065 1 1.0 1.0 nan 0 0 0 8035.89596354 0.0 0.0 -98.9954998691 2 2.0 1.0 7.44464804268 1 1 1 0.0 84070.4861979 75661.9152344 -99.0804011767 1 1.0 1.0 nan 0 0 0 11309.8386068 0.0 0.0 -101.003118017 1 1.0 1.0 nan 0 0 0 22682.028125 0.0 0.0 -101.059284262 1 1.0 1.0 nan 0 0 0 7456.7641276 0.0 0.0 -101.059667337 1 1.0 1.0 nan 0 0 0 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2824.652263720525 85.1884699938419 19.439610469587155 884.7102996182779 207.73339056150982 109.00121920548766 53.24978023564191 19.035632043933415 14.866557870963199 154.7408318971431 42.938331617576985 +batch04_S01_rep01_247_2_248_3_249 29.145804446154347 11.403257356162111 26.671321816272354 65.91472721557282 12.836481344761841 12.589077627524283 18.174340947535672 12.503269485340411 39.24309334626613 17.524176897031357 14.55250874417292 33.702422128429816 172.92629507894276 783.0955480760176 7890.742288561613 908.0847163397217 19.80037708341843 31.007337461395068 106.32318791039548 14.163165916988133 48.508016460110696 15.46594197170891 57.00207791406385 220.00847934187422 20.265189887912243 23.64314762466461 15.73938622044489 22.474819764854853 153.8046490125126 12.902672684596872 13.529289950527245 35.18005005483794 17.803237013058293 22.91072216920635 29.072511801888158 10.435581029054788 26.001983006564117 162.1758993249092 20.523978854006582 11.734970488934207 68.04667417044196 15.209997366072061 35.70823481568423 141.61804148226892 995.5159480566981 15.360056761719074 19.626739294854946 54.80574407550248 332.4198233912416 27.57146068694726 23.082504376575656 132.4055492901498 11.352536889069903 34.19246759587594 52.709599633192404 32.6931251553414 16.732183143852165 129.39223683334504 12.735173804314831 37.664226924806435 20.178098052354798 32.63022033422411 1650.12475841556 144.59618318393495 11.819937252289463 11.459531719137752 95.46652178986943 45.98850818681185 392.4324624347464 28.685306330470123 19.66277923411009 45.57751242122212 65.03369856223578 27.663583323038484 34.45283078135637 26.24089257798373 259.14730100803024 16.993272580010395 24.579201187435473 45.057380086635504 19.769360109557685 12.091783154572036 29.63671646056521 64.42305757073076 28.296074014644727 23.609207062634766 155.1323669617276 117.52891526562009 12.774927068360968 14.761445762695951 67.41343877441024 26.656919047591074 177.0126155010977 17.569721569882333 11.817399598394326 223.0044571955293 3526.0382083293966 263.4147490754906 22.028991460975703 41.00222805238901 249.86976272590354 11.42237162300078 18.59791776995712 35.34156945436025 14.238011877702322 11.289302661995595 20.939675362480823 11.52938652876898 14.148670284636568 113.37395153991798 30.49617058273766 358.7286777554346 41.224347513824036 44.238918822376824 30.905327105476847 18.246005079669917 32.321157990536726 11.764751030543003 17.96943139409716 161.90416918265475 19.544153742229074 16.42734118048151 70.83017548262067 646.9591141860177 71.68063879447885 11.671268297746115 49.64731982379532 37.00565159265913 42.83286034871188 11.52932426628371 22.962090677201655 27.44859289176055 290.6535913733465 31.68773047161383 62.67680088531491 11.468196944790535 121.15358078229941 19.171553035559757 23.262259705804468 223.97304645610822 19.119746382461162 13.010191891585634 12.533160144732772 84.52665085186352 11.999358657595645 23.38385451885196 21.708123951976614 54.443280861491054 32.58749038238159 27.284490940069862 13.252732897966391 14.525702481993328 23.3838038584064 20.32707051546949 14.538039938005511 16.828676369044985 220.24146495745495 22.09430838853324 30.024820758808584 16.170785108828955 15.862493269798813 42.28732580139026 13.52399702995943 51.33591276439305 395.2946071417642 68.84312568682064 28.643986350999295 3630.999610028613 31.991042660590484 55.450056633369876 546.0755933641905 182.0840733025534 41.59250978520138 31.80990575010578 32.195811531274494 11.590697418912091 11.395825193240068 45.26159311145779 58.49763388576406 33.46273357461692 12.998941237893646 13.038885147447058 13.509903069259614 21.08013837227028 18.311317666309577 89.9265129734 106.53471945494805 23.37536311599015 76.69939647108087 200.49225230573367 47.78644233041623 66.62160077707276 24.940088941581887 11.386196899968327 42.54436534925234 15.237082099161327 13.63603576582579 93.23941825083688 650.3651900055743 18.777507029959892 138.035814562545 38.08176346730567 12.20169222371279 131.63761137189343 39.203173988624656 14.97075981434991 25.978261386245816 19.270181242818552 21.128630855630842 54.76136776189306 15.192120491000578 16.121940831468994 12.98590780483278 13.687328272431008 22.461615744812274 24.53821393065536 16.372367422051937 55.74055916007458 16.286049449096613 12.412335455408789 11.25626577802412 552.476527126291 247.71627501660913 153.7884429505165 46.70596168901866 37.75444408713959 2497.7825988364466 82.13199686979547 17.502397199854265 777.6885047154927 181.7680519611231 95.84847856691711 46.76710816318723 14.433467449312426 11.59975438288337 306.0211220254601 83.72515304002712 \ No newline at end of file
--- a/test-data/report_pls_01.xt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/report_pls_01.xt Tue Apr 28 17:21:19 2020 -0400 @@ -1,73 +1,73 @@ filename event scans peaks median_rsd -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 125 8.16474487133 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.91689453929 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 66 7.68607124086 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 59 7.3571823389 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 38 7.81073302387 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.11304069203 -batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 6.30005138853 -batch04_B02_rep01_301.mzML SIM-Stitch NA 482 7.76858437374 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 128 8.07600991574 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 125 8.03864926779 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 65 7.44888873374 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 61 6.29657260707 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 47 7.01271931319 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.3500419991 -batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 43 7.37566447385 -batch04_B02_rep02_302.mzML SIM-Stitch NA 500 7.68715459068 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 123 9.16935154458 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.55444375891 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 66 7.78351619427 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 57 6.27056997549 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.20380544323 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 32 8.26327800306 -batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 8.21592686599 -batch04_B02_rep03_303.mzML SIM-Stitch NA 485 8.03552677192 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 79 7.03196696794 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 80 7.76766561352 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.15363335888 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 54 6.06465919921 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 38 6.24970496714 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 7.42363265295 -batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 38 7.08865209918 -batch04_QC17_rep01_262.mzML SIM-Stitch NA 369 7.18546096997 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 77 7.67971252743 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 76 7.40959870023 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.07007716689 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 53 6.56434715809 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 43 6.01206175751 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 6.89479622473 -batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 6.82339923038 -batch04_QC17_rep02_263.mzML SIM-Stitch NA 370 7.32153403689 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 76 7.06684475755 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 77 7.70812724744 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 62 7.27381932537 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 56 6.85168250471 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.1369518449 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 22 9.04310387911 -batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 44 8.17119973043 -batch04_QC17_rep03_264.mzML SIM-Stitch NA 381 7.63853989932 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 67 6.9449339373 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [140.00-240.00] 12 74 7.56562141338 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 63 7.25018452732 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.83402648161 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 46 6.86311688031 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.56433662729 -batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 47 7.38328588939 -batch04_S01_rep01_247.mzML SIM-Stitch NA 378 7.20481827147 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 68 7.61402326633 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 74 6.91382809333 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 63 7.81020674999 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 52 6.67116706795 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 49 7.47235757299 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 29 9.18092932673 -batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 7.49743321145 -batch04_S01_rep02_248.mzML SIM-Stitch NA 385 7.44772817369 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 70 8.14059659419 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 72 6.70234634239 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 60 8.31220999647 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.64301911594 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 48 6.5996960655 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.38454762189 -batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 9.08654743835 -batch04_S01_rep03_249.mzML SIM-Stitch NA 381 7.56306270833 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 125 8.164744871334845 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.9168945392902135 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 66 7.686071240864687 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 59 7.357182338903599 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 38 7.810733023874823 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.113040692029466 +batch04_B02_rep01_301.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 6.300051388534287 +batch04_B02_rep01_301.mzML SIM-Stitch NA 482 7.768584373738055 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 128 8.076009915741135 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 125 8.038649267793415 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 65 7.448888733736318 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 61 6.296572607068351 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 47 7.012719313185922 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 31 7.350041999095771 +batch04_B02_rep02_302.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 43 7.375664473847967 +batch04_B02_rep02_302.mzML SIM-Stitch NA 500 7.687154590676263 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 123 9.169351544578852 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [140.00-240.00] 10 118 7.554443758914416 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 66 7.783516194269935 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 57 6.270569975489961 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.203805443231127 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 32 8.263278003056694 +batch04_B02_rep03_303.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 45 8.21592686599179 +batch04_B02_rep03_303.mzML SIM-Stitch NA 485 8.035526771916881 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 79 7.031966967936938 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 80 7.7676656135167175 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.153633358875439 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 54 6.064659199205902 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 38 6.249704967143267 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 7.423632652950013 +batch04_QC17_rep01_262.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 38 7.08865209918093 +batch04_QC17_rep01_262.mzML SIM-Stitch NA 369 7.1854609699699745 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 77 7.679712527427614 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 76 7.4095987002251995 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 61 8.070077166892615 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 53 6.56434715809076 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 43 6.0120617575086035 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 19 6.894796224726954 +batch04_QC17_rep02_263.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 6.823399230382235 +batch04_QC17_rep02_263.mzML SIM-Stitch NA 370 7.3215340368881066 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 76 7.066844757552882 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 77 7.708127247443593 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 62 7.273819325368941 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 56 6.85168250470795 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 44 8.136951844903859 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 22 9.043103879106212 +batch04_QC17_rep03_264.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 44 8.17119973043174 +batch04_QC17_rep03_264.mzML SIM-Stitch NA 381 7.638539899322612 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 67 6.94493393729959 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [140.00-240.00] 12 74 7.565621413380442 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 63 7.250184527315313 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.834026481611651 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 46 6.8631168803092875 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.5643366272894745 +batch04_S01_rep01_247.mzML FTMS + p ESI w SIM ms [490.00-590.00] 14 47 7.383285889388576 +batch04_S01_rep01_247.mzML SIM-Stitch NA 378 7.204818271465472 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 68 7.6140232663257965 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 74 6.913828093334823 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [210.00-310.00] 15 63 7.810206749993205 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 52 6.671167067945765 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 49 7.47235757298909 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 29 9.180929326732146 +batch04_S01_rep02_248.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 7.4974332114539 +batch04_S01_rep02_248.mzML SIM-Stitch NA 385 7.447728173693162 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 70 8.140596594185261 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 72 6.7023463423858916 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 60 8.312209996466285 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [280.00-380.00] 15 51 6.643019115940489 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 48 6.599696065499092 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 30 7.38454762189305 +batch04_S01_rep03_249.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 50 9.086547438353602 +batch04_S01_rep03_249.mzML SIM-Stitch NA 381 7.563062708333447
--- a/test-data/report_pls_02.xt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/report_pls_02.xt Tue Apr 28 17:21:19 2020 -0400 @@ -1,25 +1,25 @@ filename event scans peaks median_rsd -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 62 9.10679576511 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 66 8.37633825047 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 30 13.8609519301 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 43 11.9950166441 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 32 10.1868114169 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 15 11.2326559481 -batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 24 14.1641211658 -batch04_QC18_rep01_280.mzML SIM-Stitch NA 272 10.8339327639 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 56 10.022274693 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 47 16.5074895025 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 47 10.32312253 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 46 7.96958465718 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 30 8.39097430939 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 16 9.67349503755 -batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [490.00-590.00] 12 27 9.46664767552 -batch04_QC18_rep02_281.mzML SIM-Stitch NA 269 10.0625229083 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 69 7.5232876329 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 71 7.71867980771 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 50 7.01093076419 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 49 7.24728641458 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 39 8.26255528557 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 20 8.48394726745 -batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 5.46125101547 -batch04_QC18_rep03_282.mzML SIM-Stitch NA 339 7.33323994646 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 62 9.106795765105987 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 66 8.376338250469699 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 30 13.860951930094206 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 43 11.995016644120462 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [350.00-450.00] 13 32 10.18681141686221 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 15 11.232655948051354 +batch04_QC18_rep01_280.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 24 14.164121165835418 +batch04_QC18_rep01_280.mzML SIM-Stitch NA 272 10.833932763925075 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 56 10.02227469296428 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 47 16.50748950248718 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 47 10.323122529981012 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 46 7.969584657178587 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 30 8.390974309393076 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [420.00-520.00] 12 16 9.67349503755467 +batch04_QC18_rep02_281.mzML FTMS + p ESI w SIM ms [490.00-590.00] 12 27 9.466647675517853 +batch04_QC18_rep02_281.mzML SIM-Stitch NA 269 10.06252290827951 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [70.00-170.00] 10 69 7.52328763290241 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [140.00-240.00] 11 71 7.905522565392167 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [210.00-310.00] 14 50 7.010930764188746 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [280.00-380.00] 14 49 7.247286414579351 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [350.00-450.00] 14 39 8.26255528557101 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [420.00-520.00] 13 20 8.483947267451931 +batch04_QC18_rep03_282.mzML FTMS + p ESI w SIM ms [490.00-590.00] 13 41 5.4612510154689105 +batch04_QC18_rep03_282.mzML SIM-Stitch NA 339 7.428907429907003
--- a/test-data/report_pls_rf_01.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/report_pls_rf_01.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,4 @@ name peaks peaks_3oo3 median_rsd_3oo3 -batch04_B02_rep01_301_2_302_3_303 487 421 12.3353334905 -batch04_QC17_rep01_262_2_263_3_264 364 321 7.90853836608 -batch04_S01_rep01_247_2_248_3_249 383 331 5.34421558583 +batch04_B02_rep01_301_2_302_3_303 487 421 12.335333490423352 +batch04_QC17_rep01_262_2_263_3_264 364 321 7.908538366075825 +batch04_S01_rep01_247_2_248_3_249 383 331 5.344215585775828
--- a/test-data/report_pls_rf_02.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/report_pls_rf_02.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,2 @@ name peaks peaks_3oo3 median_rsd_3oo3 -batch04_B02_rep01_301_2_302_3_303 487 421 12.3353334905 -batch04_QC17_rep01_262_2_263_3_264 364 321 7.90853836608 -batch04_S01_rep01_247_2_248_3_249 383 331 5.34421558583 +batch04_QC17_rep01_262_2_263_3_264 15 15 8.602469347435797
--- a/test-data/report_pls_rf_03.txt Sat Apr 11 16:46:21 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -name peaks peaks_3oo3 median_rsd_3oo3 -batch04_QC17_rep01_262_2_263_3_264 15 15 8.60246934744
--- a/test-data/sample_list_after_bf.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/sample_list_after_bf.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,3 +1,3 @@ filename injectionOrder replicates classLabel -batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC -batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample +batch04_QC17_rep01_262_2_263_3_264 4 1-2-3 QC +batch04_S01_rep01_247_2_248_3_249 7 1-2-3 sample
--- a/test-data/sample_list_after_mv_filter.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/sample_list_after_mv_filter.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,3 +1,3 @@ -filename classLabel -batch04_QC17_rep01_262_2_263_3_264 QC -batch04_S01_rep01_247_2_248_3_249 sample +filename injectionOrder replicates classLabel +batch04_QC17_rep01_262_2_263_3_264 4 1-2-3 QC +batch04_S01_rep01_247_2_248_3_249 7 1-2-3 sample
--- a/test-data/samplelist_1.txt Sat Apr 11 16:46:21 2020 -0400 +++ b/test-data/samplelist_1.txt Tue Apr 28 17:21:19 2020 -0400 @@ -1,4 +1,4 @@ filename injectionOrder replicates classLabel -batch04_B02_rep01_301_2_302_3_303 1 1_2_3 blank -batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC -batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample +batch04_B02_rep01_301_2_302_3_303 1 1-2-3 blank +batch04_QC17_rep01_262_2_263_3_264 4 1-2-3 QC +batch04_S01_rep01_247_2_248_3_249 7 1-2-3 sample
--- a/test-data/samplelist_2.txt Sat Apr 11 16:46:21 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -filename injectionOrder replicates classLabel -batch04_B02_rep01_301_2_302_3_303 1 1_2_3 blank -batch04_QC17_rep01_262_2_263_3_264 4 1_2_3 QC -batch04_S01_rep01_247_2_248_3_249 7 1_2_3 sample