Mercurial > repos > galaxyp > feature_alignment
changeset 9:9ad7babdbedd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
| author | galaxyp |
|---|---|
| date | Sat, 30 May 2015 05:27:37 -0400 |
| parents | 4fd8df131c3c |
| children | 23ecd1ee4422 |
| files | feature_alignment.xml test-data/feature_alignment_1_openswath_output_cluster_ids.csv test-data/feature_alignment_1_openswath_output_matrix.csv test-data/feature_alignment_2_output_1_ids.csv test-data/feature_alignment_2_output_2_matrix.csv test-data/feature_alignment_3_openswath_input.csv test-data/feature_alignment_3_openswath_output_cluster_ids.csv test-data/feature_alignment_5_peakview_output_matrix.csv test-data/feature_alignment_openswath_input_1.csv test-data/feature_alignment_peakview_input_2.csv tool_dependencies.xml |
| diffstat | 11 files changed, 213 insertions(+), 20 deletions(-) [+] |
line wrap: on
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--- a/feature_alignment.xml Thu May 21 12:47:52 2015 -0400 +++ b/feature_alignment.xml Sat May 30 05:27:37 2015 -0400 @@ -5,26 +5,37 @@ <requirement type="package" version="0.3.2">msproteomicstools</requirement> </requirements> <stdio> - <exit_code level="fatal" range="1:"/> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> </stdio> <version_command>feature_alignment.py --version</version_command> <command> <![CDATA[ feature_alignment.py --in #echo '" "'.join([ str($file) for $file in $inputs ]) # - --file_format $oformat - #if str($oformat) == "openswath": + --file_format $iformat + ##if str($iformat) == "openswath": --out $out - #end if + ##end if --out_matrix out_matrix.tsv --out_ids $out_ids --fdr_cutoff $fdr_cutoff - #if $max_fdr_quality and $max_fdr_quality is not None: - --max_fdr_quality "$max_fdr_quality" + #if $max_fdr_quality: + --max_fdr_quality $max_fdr_quality + #end if + #if $max_rt_diff: + --max_rt_diff $max_rt_diff #end if - --max_rt_diff $max_rt_diff - --iso_max_rt_diff $iso_max_rt_diff - --frac_selected $frac_selected + #if $iso_max_rt_diff: + --iso_max_rt_diff $iso_max_rt_diff + #end if + #if $frac_selected: + --frac_selected $frac_selected + #end if --method $method --matrix_output_method $matrix_output_method --realign_method $realign_method @@ -34,22 +45,22 @@ ]]></command> <inputs> - <param name="inputs" type="data" multiple="True" + <param name="inputs" type="data" multiple="True" format="txt" label="A list of mProphet output files containing all peakgroups" help="(--in)"/> - <param name="oformat" type="select" label="Which input file format is used" help="(--file_format)"> - <option value="openswath">OpenSwath</option> - <option value="peakview" selected="True">Peakview</option> + <param name="iformat" type="select" label="Which input file format is used" help="(--file_format)"> + <option value="openswath" selected="True">OpenSwath</option> + <option value="peakview">Peakview</option> </param> <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" /> - <param name="max_fdr_quality" type="text" default="-1.0" + <param name="max_fdr_quality" type="float" value="-1.0" default="-1.0" optional="True" label="Extension score cutoff" help="During the extension phase of the algorithm, peakgroups of this quality will still be considered for alignment (in FDR) - it is possible to give a range in the format lower,higher+stepsize,stepsize - e.g. 0,0.31,0.01 (-1 will set it to fdr_cutoff) (--max_fdr_quality)"/> - <param name="max_rt_diff" type="integer" value="30" default="30" + <param name="max_rt_diff" type="integer" value="30" default="30" optional="True" label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/> - <param name="iso_max_rt_diff" type="text" value="10" default="10" + <param name="iso_max_rt_diff" type="integer" value="10" default="10" optional="True" label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" /> - <param name="frac_selected" type="float" value="0.0" min="0" max="1" + <param name="frac_selected" type="float" value="0.0" min="0" max="1" optional="True" label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/> <param name="method" type="select" label="Which method to use for the clustering" @@ -88,10 +99,63 @@ <!-- Id file only containing the ids --> <data format="tabular" name="out_ids"/> <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) --> - <data format="text" name="out"> - <filter>oformat == 'openswath'</filter> + <data format="tabular" name="out"> + <!-- according to the documentation this output only works for SWATH, + but it is a requirement argument in python argparse. + So we need to output it. --> + <!--filter>iformat == 'openswath'</filter--> </data> </outputs> + <tests> + <test> + <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="method" value="best_cluster_score" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_1_openswath_output_matrix.csv" ftype="tabular" /> + <output name="out_ids" file="feature_alignment_1_openswath_output_cluster_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="method" value="best_overall" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_2_output_2_matrix.csv" ftype="tabular" /> + <output name="out_ids" file="feature_alignment_2_output_1_ids.csv" ftype="tabular" /> + </test> + <!-- needs R dependency; The python equivalent should be enough I guess. + <test> + <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="realign_method" value="splineR" /> + <param name="method" value="best_cluster_score" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="maxtrix_output_method" value="RT" /> + <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" /> + </test> + --> + <test> + <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="realign_method" value="splinePy" /> + <param name="method" value="best_cluster_score" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_peakview_input_2.csv" ftype="txt" /> + <param name="iformat" value="peakview" /> + <param name="method" value="best_cluster_score" /> + <param name="max_fdr_quality" value="0.0001" /> + <param name="fdr_cutoff" value="0.000000001" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_5_peakview_output_matrix.csv" ftype="tabular" /> + </test> + + </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_1_openswath_output_cluster_ids.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,15 @@ +f_7695999890006491586 +f_7995570933545899074 +f_13533807518639064717 +f_15970037542975291475 +f_10695898602322980677 +f_6146381832908670245 +f_17231814870828860734 +f_17124686349881931625 +f_14033255530503723792 +f_13169006090966118307 +f_17032480123683661142 +f_17254733915653094913 +f_7259477005084093710 +f_1946229642962775443 +f_1127496644798128693
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_1_openswath_output_matrix.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,2 @@ +Peptide Protein Intensity_dataset_1.dat_0_0 RT_dataset_1.dat_0_0 Intensity_dataset_1.dat_1_0 RT_dataset_1.dat_1_0 Intensity_dataset_1.dat_2_0 RT_dataset_1.dat_2_0 Intensity_dataset_1.dat_3_0 RT_dataset_1.dat_3_0 RT_mean RT_std pg_pvalue +17365_TLDTAAEKIVETATR/3_run0 Spyo_Exp3652_DDB_SeqID_324814 120.0 24.5656409693 50.0 18.2354661146 100.0 38.7373461565 130.0 36.7481804498 29.571658422550001 8.5012023683264122 1.3988719619301746e-10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_2_output_1_ids.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,4 @@ +f_7995570933545899074 +f_10695898602322980677 +f_14033255530503723792 +f_7259477005084093710
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_2_output_2_matrix.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,2 @@ +Peptide Protein Intensity_dataset_5.dat_0_0 RT_dataset_5.dat_0_0 Intensity_dataset_5.dat_1_0 RT_dataset_5.dat_1_0 Intensity_dataset_5.dat_2_0 RT_dataset_5.dat_2_0 Intensity_dataset_5.dat_3_0 RT_dataset_5.dat_3_0 RT_mean RT_std pg_pvalue +17365_TLDTAAEKIVETATR/3_run0 Spyo_Exp3652_DDB_SeqID_324814 120.0 24.5656409693 130.0 88.9418431607 100.0 38.7373461565 130.0 36.7481804498 47.248252684074998 24.675612494332714 1.201290380110036e-09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_3_openswath_input.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,33 @@ +transition_group_record decoy transition_group_id run_id filename RT id Sequence FullPeptideName ProteinName assay_rt delta_rt leftWidth norm_RT peak_apices_sum rightWidth aggr_Peak_Area peak_group_rank d_score m_score iRT_of_assay comment Charge aggr_Peak_Apex aggr_Fragment_Annotation sn_ratio Intensity +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4157.2848086113 f_14033255530503723792 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-06 61.1 cluster TRUE 2 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f_17032480123683661142 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 264.223565408 4377.25 68.7539061792 5567 4431.8701171875 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 4 -3.3249147171 0.3220580725 61.1 NA 2 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 1 150 +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4103.0075035304 f_17254733915653094913 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 -29.7116641116 4083.669921875 60.2344769173 460 4110.9799804688 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 3 -1.1571588178 0.2855822027 61.1 NA 2 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 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TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 117.7073076667 4213.3901367188 64.4992677521 13028 4264.58984375 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 -1.2538849522 0.1 61.1 cluster FALSE 2 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 60 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 5002.5892306441 f_17231814870828860734 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 277.5401886459 4384.080078125 69.1211247371 6969 4425.0400390625 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 4 -2.1006079776 0.3411849331 61.1 NA 2 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 1 40 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4550.661382069 f_17124686349881931625 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 -174.3876599292 3943.6899414063 56.0528131928 610 3960.7600097656 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 3 -1.1356280226 0.3069359946 61.1 NA 2 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 1 20 +pg1 FALSE trgr1 0 split_hroest_K120808_combined.featureXML 100 1 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 1 split_hroest_K120808_combined.featureXML 200 2 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 2 split_hroest_K120808_combined.featureXML 300 3 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 3 split_hroest_K120808_combined.featureXML 400 4 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 0 split_hroest_K120808_combined.featureXML 5000 5 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 1 split_hroest_K120808_combined.featureXML 5200 6 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 2 split_hroest_K120808_combined.featureXML 5400 7 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 3 split_hroest_K120808_combined.featureXML 5600 8 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 0 split_hroest_K120808_combined.featureXML 2000 9 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 1 split_hroest_K120808_combined.featureXML 2100 10 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 2 split_hroest_K120808_combined.featureXML 2300 11 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 3 split_hroest_K120808_combined.featureXML 2500 12 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 0 split_hroest_K120808_combined.featureXML 2100 9 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 1 split_hroest_K120808_combined.featureXML 2200 10 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 2 split_hroest_K120808_combined.featureXML 2400 11 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 3 split_hroest_K120808_combined.featureXML 2600 12 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_3_openswath_output_cluster_ids.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,31 @@ +7 +8 +5 +6 +11 +12 +9 +10 +f_7695999890006491586 +f_7995570933545899074 +f_13533807518639064717 +f_15970037542975291475 +f_10695898602322980677 +f_6146381832908670245 +f_17231814870828860734 +f_17124686349881931625 +f_14033255530503723792 +f_13169006090966118307 +f_17032480123683661142 +f_17254733915653094913 +f_7259477005084093710 +f_1946229642962775443 +f_1127496644798128693 +3 +4 +1 +2 +11 +12 +9 +10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_5_peakview_output_matrix.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,3 @@ +Peptide Protein Intensity_dataset_13.dat_ywu_L121218_002_SW.wiff (sample 1)_0 RT_dataset_13.dat_ywu_L121218_002_SW.wiff (sample 1)_0 Intensity_dataset_13.dat_ywu_L121218_003_SW.wiff (sample 1)_0 RT_dataset_13.dat_ywu_L121218_003_SW.wiff (sample 1)_0 Intensity_dataset_13.dat_ywu_L121218_004_SW.wiff (sample 1)_0 RT_dataset_13.dat_ywu_L121218_004_SW.wiff (sample 1)_0 Intensity_dataset_13.dat_ywu_L121218_005_SW.wiff (sample 1)_0 RT_dataset_13.dat_ywu_L121218_005_SW.wiff (sample 1)_0 Intensity_dataset_13.dat_ywu_L121218_006_SW.wiff (sample 1)_0 RT_dataset_13.dat_ywu_L121218_006_SW.wiff (sample 1)_0 RT_mean RT_std pg_pvalue +LIGNMALLPLR+2 Actin-related protein 2/3 complex subunit 3 musculus 2900.0 80.41 3700.0 80.3267592431513 2300.0 80.2970686001864 2300.0 80.385140821583 3200.0 80.3699472702056 80.357783187025262 0.040673693694963493 1.0 +LIGNMALLPLR+3 Actin-related protein 2/3 complex subunit 3 musculus 150.0 80.33 97.0 80.3372300313998 140.0 80.3072715711995 120.0 80.3546761207408 98.0 80.2433156865484 80.314498681977696 0.038705249414076479 1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_openswath_input_1.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,17 @@ +transition_group_record decoy transition_group_id run_id filename RT id Sequence FullPeptideName ProteinName assay_rt delta_rt leftWidth norm_RT peak_apices_sum rightWidth aggr_Peak_Area peak_group_rank d_score m_score iRT_of_assay comment Charge aggr_Peak_Apex aggr_Fragment_Annotation sn_ratio Intensity Comment: The following columns are for mProphet Tr iRT_empirical iRT_predicted protein transition_group_pepseq +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4157.2848086113 f_14033255530503723792 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-06 61.1 cluster TRUE 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 4157.2848086113 4157.2848086113 4147.2848086113 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4236.7508741707 f_13169006090966118307 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 104.0317065287 4199.740234375 64.1108995811 8628 4261.1899414063 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 2 -3.1954820554 0.0005 61.1 cluster FALSE 2 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 1 250 4236.7508741707 4236.7508741707 4226.7508741707 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4396.94273305 f_17032480123683661142 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 264.223565408 4377.25 68.7539061792 5567 4431.8701171875 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 4 -3.3249147171 0.3220580725 61.1 NA 2 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 1 150 4396.94273305 4396.94273305 4386.94273305 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4103.0075035304 f_17254733915653094913 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 -29.7116641116 4083.669921875 60.2344769173 460 4110.9799804688 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 3 -1.1571588178 0.2855822027 61.1 NA 2 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 1 180 4103.0075035304 4103.0075035304 4093.0075035304 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4237.834612717 f_7259477005084093710 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 88.9418431607 4220.2099609375 63.6912797891 5950 4257.759765625 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 1 -1.2978089457 0.005 61.1 cluster FALSE but FDR below 1% 2 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 1 130 4237.834612717 4237.834612717 4227.834612717 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4167.1282356709 f_1946229642962775443 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 18.2354661146 4128.0400390625 61.629163735 967 4196.3198242188 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 2 1.2528426368 0.0590706643 61.1 cluster TRUE 2 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 1 50 4167.1282356709 4167.1282356709 4157.1282356709 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4204.9589978683 f_546336782280825114 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 56.0662283119 4199.7299804688 62.7324789567 180 4216.7998046875 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 4 -1.9709294327 0.3276775879 61.1 NA 2 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 1 220 4204.9589978683 4204.9589978683 4194.9589978683 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 3949.633676731 f_1127496644798128693 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 -199.2590928254 3933.4499511719 55.2860439144 381 3957.3500976563 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 3 -1.8881030993 0.325723046 61.1 NA 2 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 1 120 3949.633676731 3949.633676731 3939.633676731 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4457.7861318076 f_7695999890006491586 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 270.9862086544 4438.6899414063 68.9583866448 3605 4486.4799804688 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 4 -1.8914462466 0.3350264606 61.1 NA 2 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 1 130 4457.7861318076 4457.7861318076 4447.7861318076 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4225.5372693098 f_7995570933545899074 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 38.7373461565 4199.7202148438 62.2205422539 997 4250.9301757813 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 2 0.440521846 0.3 61.1 cluster TRUE 2 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1 100 4225.5372693098 4225.5372693098 4215.5372693098 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4297.2778585929 f_13533807518639064717 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 110.4779354397 4261.169921875 64.3018309281 5641 4315.7900390625 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 -1.4000010917 0.15 61.1 cluster FALSE 2 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 80 4297.2778585929 4297.2778585929 4287.2778585929 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4000.5531316006 f_15970037542975291475 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 -186.2467915526 3988.0700683594 55.6934570662 512 4011.9599609375 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 3 -1.6324942375 0.3278895544 61.1 NA 2 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 1 20 4000.5531316006 4000.5531316006 3990.5531316006 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4161.797222448 f_10695898602322980677 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 36.7481804498 4134.8701171875 62.1581880861 1624 4186.080078125 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 2 2.8268775648 0.1 61.1 cluster TRUE 2 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 1 130 4161.797222448 4161.797222448 4151.797222448 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4242.7563496649 f_6146381832908670245 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 117.7073076667 4213.3901367188 64.4992677521 13028 4264.58984375 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 -1.2538849522 0.1 61.1 cluster FALSE 2 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 60 4242.7563496649 4242.7563496649 4232.7563496649 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4402.5892306441 f_17231814870828860734 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 277.5401886459 4384.080078125 69.1211247371 6969 4425.0400390625 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 4 -2.1006079776 0.3411849331 61.1 NA 2 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 1 40 4402.5892306441 4402.5892306441 4392.5892306441 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 3950.661382069 f_17124686349881931625 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 -174.3876599292 3943.6899414063 56.0528131928 610 3960.7600097656 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 3 -1.1356280226 0.3069359946 61.1 NA 2 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 1 20 3950.661382069 3950.661382069 3940.661382069 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_peakview_input_2.csv Sat May 30 05:27:37 2015 -0400 @@ -0,0 +1,22 @@ +"Time" "peakGroup" "Sample" "Pep.Index" "Protein" "Decoy" "Peptide" "Confidence" "Precursor.MZ" "Precursor.Charge" "Peak.RT" "Transition.Areas" "Average.Peak" "Median.RT" "MaxPeak.RT" "MaxPeak.Intensity" "Score" "AbsoluteMzError" "MedianMzError" "RtConsistency" "ExpectedRt" "ChroWidthConsistency" "IntensityPattern" "YIons" "MatchProbability" "SignalToNoise" "HLIntensityCorrelation" "Xcorr2DPeaks" "Num.Prerranked.groups" "Num.Evaluated.groups" "Preranking" "RT" "ExpectedRT" "RTHeight" "ExpectedRTHeight" "RT50Width" "RTNoise" "NumRTPeaksAboveSN" "MZ" "ExpectedMZ" "MZHeight" "MZ50Width" "Charge" "ExpectedCharge" "Mono" "Used" "YIonMZ" "ExpectedYIons" "X" "aligned_rt" "aligned_rt_diff" +"11:23:15" 1 "ywu_L121218_002_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9226304650383 "611.4239_y5:null_null_null,498.3398_y4:2033.1569058655_151.076127468725_8.85330715163171,713.4014_b7:1365.37315120079_70_5.18589778942739,600.3174_b6:1359.22114090841_123.833655084656_6.17151478387135,529.2803_b5:null_null_null,682.461_y6:null_null_null," "80.05:10,80.19:176,80.22:351.9,80.45:176,80.62:3" 80.33 80.27 150 1.9e+08 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.73 0.53 0.13 1 1 1 "80.3875450179245_80.2681172911531_80.3242628231043_80.3408775664709_80.3491145712847_80.2517647442096" 79.9226304650383 "93.2277914764818_151.076127468725_70_123.833655084656_66.6648179751019_81" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.138196816636594_0.256866657170733_0.350689583333335_0.232522379159306_0.318119040562934_0.387719615516488" "4.95061404883585_8.85330715163171_5.18589778942739_6.17151478387135_5.99752823804411_4.55081763169696" "1_1_1_1_2_1" "611.422011040799_498.348530307152_713.409665210068_600.319850643079_529.289683045948_682.44857252014" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.6666666666667_13.3333333333333_13.3333333333333_20.3333333333333_13.3333333333333_20.3333333333333" "0.0160945543258322_0.0488412904473989_0.0358163514524676_0.0173936213901698_0.00974217047485126_0.00661567511519934" "1_1_1_1_2_1" "1_1_1_1_1_1" "False_True_True_True_True_False" "True_True_True_True_True_True" "0_288.213417469409_385.259600476745_498.348530307152_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.33 0 +"11:45:05" 1 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:63172.9695350965_2913.21957472496_32.6363403871121,682.461_y6:27701.8619944977_1377.43938585543_8.62548016272112,813.5015_y7:6817.05357691055_561.21992990478_20.6417114060844,927.5444_y8:6259.08450213339_255.668467680939_22.7189417125541,826.4855_b8:null_null_null,713.4014_b7:2489.71458466376_294.551253757974_41.7198927051708," "80.01:450.6,80.2:2935.3,80.46:5870.5,80.55:2935.3,80.69:470.2" 80.41 80.38 2900 8.5e+11 0.054 0.074 0.03 0.089 0.14 0.02 0.0099 0.035 1 0.5 0.23 18 3 1 "80.3847265781083_80.3635034220867_80.4302157655778_80.3627289651931_80.4304769279579_80.4789452144931" 79.9217331132498 "2913.21957472496_1377.43938585543_561.21992990478_255.668467680939_430.552794744168_294.551253757974" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.328344360247897_0.331599877802205_0.197121681696942_0.482989703137633_0.482827452321217_0.158959141540507" "32.6363403871121_8.62548016272112_20.6417114060844_22.7189417125541_30.1972793139185_41.7198927051708" "3_1_2_4_2_5" "984.540922640428_682.467753766226_813.511891732749_927.557670439387_826.501929646604_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "168.333333333333_131_61.3333333333333_30.6666666666667_13.6666666666667_N/A" "0.0076031054517216_0.0457597515854786_0.0374294178778882_0.029309592705431_0.0324639638558892_N/A" "0_1_1_1_1_0" "1_1_1_1_1_1" "Unknown_True_True_True_False_Unknown" "True_True_True_True_True_True" "175.14154928442_288.17524862357_385.259246937153_498.347439687727_611.424923681304_682.467753766226_813.511891732749_927.557670439387_984.540922640428_1097.64646750353_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.41 0 +"11:45:05" 2 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:26415.0318094871_1505.72434561968_31.2090056959494,713.4014_b7:null_null_null," "78.92:92.8,79.11:814.4,79.2:1628.7,79.41:814.4,79.6:165.3" 79.23 79.24 1500 210000 0.5 0.5 0.75 0.089 0.5 0.75 0.79 0.52 0.005 0.5 0.75 18 3 2 "79.2280349897488_N/A_N/A_79.2267074012329_79.2366567324793_N/A" 79.9217331132498 "9165.04035107153_N/A_N/A_1142.347612787_1505.72434561968_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.289693645651596_N/A_N/A_0.272703094160448_0.300779618806786_N/A" "30.595322958426_N/A_N/A_21.6487619093028_31.2090056959494_N/A" "1_N/A_N/A_1_1_N/A" "984.583643522916_682.439745778068_813.462829826501_927.560190138688_826.487700788133_713.332836640461" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "1026_17_17.0000000002328_139_169_20.3333333333333" "0.0528225874248847_0.00915705196894123_0.00419014783278726_0.061628638481011_0.0583090823893144_0.0152053454114593" "1_2_0_1_0_5" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_False" "True_False_False_True_True_False" "175.11498948848_288.172165486245_0_0_0_682.419638638861_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.23 0 +"11:45:05" 3 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:1616.42988483826_131.233156543058_21.2872124526729,682.461_y6:1300.21980511359_95.9807853822131_6.67305574172559,813.5015_y7:840.098846386696_132.276870446228_20.5933104277774,927.5444_y8:373.882902853722_72.6421801600245_18.8812537139364,826.4855_b8:675.788180660378_163.110710100234_24.663600700104,713.4014_b7:null_null_null," "75.71:392.1,75.74:463,75.88:925.9,75.92:463,76.05:289.6" 75.83 75.77 160 45000 0.5 0.5 0.079 0.52 0.47 0.37 0.55 0.19 0.64 0.5 0.36 18 3 3 "75.8303010940226_75.9070595744131_75.9403833333333_75.7686_75.7686_75.8341911820244" 79.9217331132498 "131.233156543058_95.9807853822131_132.276870446228_72.6421801600245_163.110710100234_383.871236201916" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.214956620442308_0.228138567048632_0.0911129845835745_0.0797467732449491_0.0691309903446609_0.468465832653436" "21.2872124526729_6.67305574172559_20.5933104277774_18.8812537139364_24.663600700104_43.7497137357593" "7_3_8_15_6_4" "984.560648952255_N/A_813.483650376649_N/A_N/A_713.391815610818" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "34_N/A_16.6666666666667_N/A_N/A_30.3333333332557" "0.00557728288197268_N/A_0.0327104558474502_N/A_N/A_0.00377009978888054" "0_0_1_0_0_3" "1_1_1_1_1_1" "Unknown_Unknown_True_Unknown_Unknown_False" "True_True_True_True_True_True" "0_288.222821731842_0_498.274877624178_611.370451935052_0_813.483650376649_0_984.560648952255_1097.57090085832_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.83 0 +"12:21:59" 1 "ywu_L121218_003_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.4599885783973 "611.4239_y5:695.955480627102_81.5958365448391_3.92152729414383,498.3398_y4:2243.25091199125_97.2531292215032_4.25943739856399,713.4014_b7:534.424645320621_50.6392833808782_5.91082136540284,600.3174_b6:801.413919946023_87.4041774769889_5.92348122073576,529.2803_b5:798.734694509919_60_6.99582870957075,682.461_y6:null_null_null," "79.53:40,79.61:203.9,79.76:407.8,79.85:203.9,79.99:20.2" 79.75 79.71 97 3.3e+09 0.5 0.5 0.05 0.13 0.05 0.05 0.05 0.075 0.83 0.5 0.05 1 1 1 "79.7691692602483_79.7130270329789_79.7873518870944_79.7355352702599_79.7529370487846_N/A" 79.4599885783973 "81.5958365448391_97.2531292215032_50.6392833808782_87.4041774769889_60_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.107360617963792_0.280681766658262_0.204320329342025_0.180310757496116_0.340557962256085_N/A" "3.92152729414383_4.25943739856399_5.91082136540284_5.92348122073576_6.99582870957075_N/A" "1_1_1_1_3_N/A" "611.418595146455_498.342011099309_N/A_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.3333333333333_20_N/A_N/A_N/A_N/A" "0.0261766851290304_0.0237477931120793_N/A_N/A_N/A_N/A" "1_1_0_0_0_0" "1_1_1_1_1_1" "True_True_Unknown_Unknown_Unknown_Unknown" "True_True_True_True_True_False" "175.112053679092_0_385.264683849443_498.342011099309_611.418595146455_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3372300313998 -0.587230031399798 +"12:46:07" 1 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:62342.0136655603_3725.01197116701_35.7878492666171,682.461_y6:31194.2841276724_1510.20616405492_8.31637249686309,813.5015_y7:17403.6864015132_679.389066434029_16.3739140748602,927.5444_y8:5519.99473730796_375.366186119185_20.4467322079474,826.4855_b8:9659.95632589417_647.450474018238_32.0915835709068,713.4014_b7:null_null_null," "79.26:234.4,79.59:3631,79.78:7262,79.84:3631,80.01:378" 79.74 79.76 3700 1e+14 0.04 0.12 0.064 0.054 0.17 0.059 0.015 0.02 0.005 0.5 0.079 19 3 1 "79.7644577758905_79.736637618253_79.6580663228811_79.7277414786923_79.7445548837875_79.7672655310848" 79.4590914543314 "3725.01197116701_1510.20616405492_679.389066434029_375.366186119185_647.450474018238_454.98845996843" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.252816287122201_0.322681716367526_0.533268176929752_0.250343589188574_0.202465161099397_0.115193810826725" "35.7878492666171_8.31637249686309_16.3739140748602_20.4467322079474_32.0915835709068_51.1608860889051" "3_1_1_2_2_6" "984.536780957495_682.463636500082_813.507963873021_927.559458911263_826.478931662218_713.40785184937" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "92_193.666666666667_68.3333333333333_40.6666666666667_34.3333333330229_17" "0.0276704712633773_0.0404383442378276_0.0640770868197933_0.0118932230194559_0.00286275658686463_0.0188505919459203" "1_1_1_1_0_2" "1_1_1_1_1_1" "True_True_True_True_Unknown_False" "True_True_True_True_True_True" "175.136478361909_288.219494139316_385.261722178417_498.341615915194_611.425582744104_682.463636500082_813.507963873021_927.559458911263_984.536780957495_1097.66028200887_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3267592431513 -0.586759243151263 +"12:46:07" 2 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:29093.9585385698_1776.12676050086_32.0297652471469,713.4014_b7:null_null_null," "78.46:130.6,78.65:944.6,78.8:1889.2,78.92:944.6,79.15:95.5" 78.75 78.76 1800 1200000 0.34 0.36 0.75 0.079 0.5 0.75 0.29 0.57 0.005 0.5 0.75 19 3 2 "78.7516732973404_N/A_N/A_78.7550152573598_78.7610379920924_N/A" 79.4590914543314 "10741.5857445992_N/A_N/A_1246.10699307787_1776.12676050086_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.221542651828784_N/A_N/A_0.201619487133527_0.27424393414789_N/A" "34.7194778603106_N/A_N/A_21.0092462057853_32.0297652471469_N/A" "1_N/A_N/A_1_1_N/A" "984.580681795204_682.412940381784_N/A_927.554781758257_826.486868259013_713.454301638241" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "1048.66666666667_54.6666666666667_N/A_130.666666666667_165_16.9999999997672" "0.0571396809709768_0.0146609016740058_N/A_0.0544077444664026_0.0564364522343794_0.00384563761019763" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.115723500999_288.140261041746_385.20544320406_498.307462939696_0_682.412940381784_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2581620805884 -0.508162080588434 +"12:46:07" 3 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:691.792131017952_86.7456409023798_20.2324044441414,826.4855_b8:null_null_null,713.4014_b7:null_null_null," "75.42:65.3,75.44:61.8,75.48:123.6,75.62:61.8,75.65:25.3" 75.55 75.55 87 700 0.5 0.5 0.75 0.52 0.5 0.75 0.79 0.94 0.14 0.5 0.75 19 3 3 "75.515728211372_N/A_N/A_75.5542535029337_75.5291360931461_75.5490535702549" 79.4590914543314 "159.55142461883_N/A_N/A_86.7456409023798_153.566740036464_589.545536155857" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.233981881483984_N/A_N/A_0.181763038584251_0.203343671103326_0.211959115150307" "33.3173351222639_N/A_N/A_20.2324044441414_29.8936920366768_45.1053314143605" "6_N/A_N/A_13_10_3" "984.562623822968_682.449936903196_N/A_927.555999078148_826.472048592545_713.397062064111" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "17_13.3333333333333_N/A_17_20.6666666666667_47.6666666666667" "0.0193737662615376_0.00860394757592076_N/A_0.0341759906041261_0.0121736639329129_0.011965251708034" "2_1_0_1_2_4" "1_1_1_1_1_1" "False_False_Unknown_True_False_False" "True_False_False_True_True_True" "0_0_385.261526700595_498.339646411046_0_0_0_927.555999078148_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.868341077206 -0.318341077205986 +"13:22:36" 1 "ywu_L121218_004_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.5941352903303 "611.4239_y5:981.529311549473_85.6745843821705_4.28290555684228,498.3398_y4:2929.44226409681_136.365977283862_8.34150108955811,713.4014_b7:946.500696399436_102.958269334049_5.14035968205949,600.3174_b6:985.500645026059_69.5706747125369_6.26787860726159,529.2803_b5:1228.13210503255_78.8876311302884_6.32066783717301,682.461_y6:null_null_null," "79.59:20,79.65:248.2,79.82:496.4,79.95:248.2,80.05:27.9" 79.82 79.78 140 2.1e+09 0.5 0.5 0.05 0.075 0.05 0.05 0.13 0.075 0.88 0.5 0.05 1 1 1 "79.8672435017827_79.7753312858912_79.822602587473_79.7341166556411_79.8169180816553_N/A" 79.5941352903303 "85.6745843821705_136.365977283862_102.958269334049_69.5706747125369_78.8876311302884_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.2207251287725_0.462644753675093_0.0981768021016762_0.283719440970074_0.300852034803768_N/A" "4.28290555684228_8.34150108955811_5.14035968205949_6.26787860726159_6.32066783717301_N/A" "1_1_1_1_2_N/A" "N/A_498.345883997847_N/A_600.31381437701_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "N/A_17_N/A_13.666666666657_N/A_N/A" "N/A_0.0128009741875417_N/A_0.0171189848325639_N/A_N/A" "0_1_0_1_0_0" "1_1_1_1_1_1" "Unknown_True_Unknown_True_Unknown_Unknown" "True_True_True_True_True_False" "0_0_385.25028700361_498.345883997847_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3072715711995 -0.487271571199457 +"13:44:11" 1 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:59350.8897150608_2346.981786619_37.9850649135046,682.461_y6:25402.5280414736_1045.80405098809_9.24410350622813,813.5015_y7:null_null_null,927.5444_y8:6720.00225295179_341.829994810099_22.500243015707,826.4855_b8:7962.23771878778_351.679036694103_27.9535393342726,713.4014_b7:3370.9048792541_310.987177223065_50.5129761020436," "79.38:462.8,79.65:2471.1,79.89:4942.3,79.99:2471.1,80.12:587.3" 79.81 79.87 2300 2.2e+12 0.02 0.035 0.054 0.035 0.064 0.059 0.054 0.045 0.96 0.5 0.079 19 3 1 "79.8655754146358_79.8125854686426_N/A_79.8072962597494_79.8068814119591_79.8342454526662" 79.5932466525774 "2346.981786619_1045.80405098809_N/A_341.829994810099_351.679036694103_310.987177223065" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.460607016991432_0.372185583367596_N/A_0.337054687245228_0.284042639751561_0.198687224187736" "37.9850649135046_9.24410350622813_N/A_22.500243015707_27.9535393342726_50.5129761020436" "3_1_N/A_3_2_8" "984.54412171768_682.459661149262_813.505010674639_927.541877166025_826.479639562907_713.399278756883" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "66.6666666666667_129.333333333333_47.3333333333333_34_58_48.3333333334886" "0.0203211645107331_0.0457507127225654_0.0172405581129169_0.0236701516765834_0.0110095043589808_0.00377008711996041" "0_1_1_1_0_0" "1_1_1_1_1_1" "Unknown_True_True_True_Unknown_Unknown" "True_True_False_True_True_True" "175.094242661756_0_385.257400075649_498.346535478075_0_682.459661149262_813.505010674639_927.541877166025_984.54412171768_1097.64207812938_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.2970686001864 -0.487068600186447 +"13:44:11" 2 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:26988.3571806801_1242.06579174239_28.1463102270691,713.4014_b7:null_null_null," "78.4:80,78.61:671.2,78.69:1342.4,78.99:671.2,79.15:132.9" 78.75 78.77 1200 240000 0.5 0.5 0.75 0.1 0.5 0.75 0.55 0.56 0.005 0.5 0.75 19 3 2 "78.7709618895227_N/A_N/A_78.7362705149892_78.7665756385286_N/A" 79.5932466525774 "8200.54297293411_N/A_N/A_1046.46993273883_1242.06579174239_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.364551540637535_N/A_N/A_0.311138762997999_0.387639946441894_N/A" "34.0759603040267_N/A_N/A_22.6269080936769_28.1463102270691_N/A" "1_N/A_N/A_1_1_N/A" "984.579576585091_682.416911372046_N/A_927.55151614531_826.486656597102_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "788.333333333333_30.6666666666279_N/A_99.3333333333333_133_N/A" "0.0549850992857728_0.0110619424380047_N/A_0.0522652403715256_0.0330430027009925_N/A" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.118294298464_288.171120788381_0_498.261175365341_0_682.416911372046_0_927.487720887883_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2236940972108 -0.473694097210839 +"13:44:11" 3 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:null_null_null,682.461_y6:487.622841645393_67.838204803993_10.1878758557517,813.5015_y7:1251.42638959628_83.99640834848_15.2696454208248,927.5444_y8:802.530857351084_94.9514553355621_23.3873732406492,826.4855_b8:2116.82682057388_93.8999939045934_24.9992358409247,713.4014_b7:8400.96587037062_361.441398078293_42.7967568687811," "75.54:366.2,75.63:549,75.71:1098,75.88:549,75.88:382.6" 75.72 75.73 360 110000 0.5 0.5 0.064 0.5 0.33 0.49 0.39 0.38 0.41 0.5 0.23 19 3 3 "75.7413648403638_75.7125397592966_75.7797150693882_75.7102065610464_75.6818057434095_75.7257400175026" 79.5932466525774 "95.4169912035431_67.838204803993_83.99640834848_94.9514553355621_93.8999939045934_361.441398078293" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.111815963110161_0.103571761493953_0.298491938261336_0.128106561858687_0.375088371585207_0.508762750205463" "24.1539043280043_10.1878758557517_15.2696454208248_23.3873732406492_24.9992358409247_42.7967568687811" "8_10_10_15_14_4" "984.534676918139_N/A_N/A_927.547362333476_N/A_713.421618928001" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "20_N/A_N/A_13.6666666666279_N/A_17.3333333333721" "0.0169492559898572_N/A_N/A_0.0113711962044363_N/A_0.00735180586298156" "2_0_0_0_0_0" "1_1_1_1_1_1" "False_Unknown_Unknown_Unknown_Unknown_Unknown" "True_True_True_True_True_True" "0_288.211043636487_385.264512219043_498.252009977079_611.364062894888_0_0_927.547362333476_984.521573915163_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.9045088180345 -0.184508818034487 +"14:20:24" 1 "ywu_L121218_005_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9022825324857 "611.4239_y5:null_null_null,498.3398_y4:1957.59662571505_71_3.61550816886865,713.4014_b7:1218.25696633481_121.84400798392_3.58936646398049,600.3174_b6:1226.6347800692_96.5584103096044_5.23123217996062,529.2803_b5:null_null_null,682.461_y6:null_null_null," "79.88:,80.06:144.7,80.22:289.4,80.25:144.7,80.39:" 80.16 80.16 120 1300000 0.53 0.53 0.13 0.13 1.1 0.13 0.13 0.13 0.8 0.53 0.13 2 2 1 "80.1896334837763_80.1190874613199_80.1636833333333_80.1791221816136_N/A_N/A" 79.9022825324857 "88.5903776759515_71_121.84400798392_96.5584103096044_N/A_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.141058315271366_0.538021041320476_0.0891532295453175_0.186385159239165_N/A_N/A" "4.799543168614_3.61550816886865_3.58936646398049_5.23123217996062_N/A_N/A" "1_1_1_1_N/A_N/A" "611.423457785713_498.341442700864_713.417449795644_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "20.3333333333333_13.6666666666667_13.3333333333333_N/A_N/A_N/A" "0.0212835904377471_0.00615193294339633_0.00754028676976759_N/A_N/A_N/A" "1_0_1_0_0_0" "1_1_1_1_1_1" "False_Unknown_True_Unknown_Unknown_Unknown" "True_True_True_True_False_False" "175.113007915228_288.210964140498_385.257060097493_498.341442700864_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3546761207408 -0.194676120740766 +"14:20:24" 2 "ywu_L121218_005_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9022825324857 "611.4239_y5:237.139918345548_50_5.81089025078037,498.3398_y4:null_null_null,713.4014_b7:null_null_null,600.3174_b6:null_null_null,529.2803_b5:604.822733679008_50_5.84875423484373,682.461_y6:null_null_null," "76.9:10,76.95:55,76.99:110,77.1:55,77.16:10" 77.02 77.07 50 18000 0.5 0.5 0.5 0.25 0.5 0.5 0.13 0.78 0.3 0.5 0.5 2 2 2 "77.0718166666667_N/A_N/A_N/A_76.9653454548867_N/A" 79.9022825324857 "50_N/A_N/A_N/A_50_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.0748460510710487_N/A_N/A_N/A_0.227524141302524_N/A" "5.81089025078037_N/A_N/A_N/A_5.84875423484373_N/A" "2_N/A_N/A_N/A_3_N/A" "611.399733556906_N/A_N/A_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.6666666667443_N/A_N/A_N/A_N/A_N/A" "0.003407076373378_N/A_N/A_N/A_N/A_N/A" "0_0_0_0_0_0" "1_1_1_1_1_1" "Unknown_Unknown_Unknown_Unknown_Unknown_Unknown" "True_False_False_False_True_False" "175.11612482527_288.20391954051_0_0_611.399733556906_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 76.9363785388898 0.0836214611102264 +"14:41:58" 1 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:54504.2487947933_2346.89844194463_28.2652353191458,682.461_y6:23900.2853571278_1136.37611113786_8.83212333560757,813.5015_y7:16462.999754284_479.947501717744_15.7459166107246,927.5444_y8:2808.87298979646_211.166251296316_21.7672255119924,826.4855_b8:12843.7825090803_344.456091861769_26.8421456405486,713.4014_b7:6386.29443529435_346.966277724737_39.1336618238081," "79.81:586.1,80.02:2708.8,80.15:5417.6,80.39:2708.8,80.55:544.3" 80.19 80.21 2300 3.4e+12 0.015 0.03 0.02 0.054 0.3 0.045 0.015 0.025 1 0.5 0.25 17 3 1 "80.2055254761197_80.1678005775601_80.1236157452456_80.1298752652172_80.3453169673917_80.2766031443511" 79.9013811937706 "2346.89844194463_1136.37611113786_479.947501717744_211.166251296316_344.456091861769_346.966277724737" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.386429353702596_0.345192643361528_0.638635527453815_0.289176323871828_1.0089259828532_0.421858940854634" "28.2652353191458_8.83212333560757_15.7459166107246_21.7672255119924_26.8421456405486_39.1336618238081" "3_1_1_3_2_5" "984.561188358471_682.459757169908_813.502558690091_927.545028427178_826.481568312005_713.414426592075" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "154_128_58_27.6666666666667_31.3333333330229_17.6666666666667" "0.0567411016096457_0.0406922873836493_0.0486266667712698_0.0595571596061291_0.00596002034103549_0.017680927771039" "1_1_1_1_0_1" "1_1_1_1_1_1" "True_True_True_True_Unknown_True" "True_True_True_True_True_True" "175.146381438637_288.169958659576_385.25952207415_498.340892378339_0_682.459757169908_813.502558690091_927.545028427178_984.561188358471_1097.65594185049_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.385140821583 -0.195140821582996 +"14:41:58" 2 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:1971.74513686026_188.967749435471_24.6808895619121,826.4855_b8:276.294621487137_80.423408961467_24.892510709682,713.4014_b7:828.629806500073_96.465899249044_30.5272604380943," "84.13:309.4,84.13:308.2,84.19:616.4,84.29:308.2,84.36:185" 84.21 84.17 190 280000 0.5 0.5 0.45 0.59 0.28 0.4 0.15 0.63 0.025 0.5 0.41 17 3 3 "84.1093848762754_N/A_N/A_84.1697364072487_84.2425333333333_84.2597481405261" 79.9013811937706 "93.4177538816948_N/A_N/A_188.967749435471_80.423408961467_96.465899249044" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.0965222044969778_N/A_N/A_0.189356602081119_0.0572815629052883_0.184135559569626" "16.8237649871685_N/A_N/A_24.6808895619121_24.892510709682_30.5272604380943" "7_N/A_N/A_6_17_11" "984.577840105363_N/A_N/A_927.4892316412_N/A_713.382206763948" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "20.3333333333333_N/A_N/A_51.3333333333333_N/A_24.6666666665114" "0.0217094817319321_N/A_N/A_0.0460492398619863_N/A_0.00221415268822511" "1_0_0_1_0_0" "1_1_1_1_1_1" "False_Unknown_Unknown_True_Unknown_Unknown" "True_False_False_True_True_True" "175.081038268756_0_385.269250122434_0_611.408819829957_682.385422670494_0_927.4892316412_984.520203718785_1097.62631108442_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 84.5889756066712 -0.378975606671162 +"14:41:58" 3 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:27214.5880128003_1619.62210021012_27.0185402209066,713.4014_b7:null_null_null," "78.75:96.1,79.03:857,79.09:1714,79.24:857,79.6:91.8" 79.12 79.13 1600 170000 0.5 0.5 0.75 0.094 0.5 0.75 0.98 0.47 0.005 0.5 0.75 17 3 2 "79.1125003656006_N/A_N/A_79.1000430920699_79.1308137268277_N/A" 79.9013811937706 "8724.7220556348_N/A_N/A_1098.94642173841_1619.62210021012_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.30529645043265_N/A_N/A_0.28974172985771_0.207437748411635_N/A" "28.9149839908288_N/A_N/A_22.3764494040067_27.0185402209066_N/A" "1_N/A_N/A_1_1_N/A" "984.579444474793_682.4129949412_N/A_927.559248908603_826.490960645532_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "845.666666666667_20.3333333333333_N/A_95.6666666666667_145.666666666667_N/A" "0.0592007849844549_0.0323979559369718_N/A_0.0589224094388783_0.0501346478230289_N/A" "1_5_0_1_0_0" "1_1_1_1_1_1" "False_False_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.111045764841_0_0_498.312993927756_0_0_0_0_984.509911839606_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2713192717295 -0.151319271729491 +"15:17:17" 1 "ywu_L121218_006_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.3525458229509 "611.4239_y5:1351.40506787869_90_5.66958929140032,498.3398_y4:2028.06882500123_97.6219697496854_4.57339987647979,713.4014_b7:1104.08944174806_88.7463292320892_5.71095956606776,600.3174_b6:1145.43396175162_91_5.95762734469545,529.2803_b5:376.288704810932_72.4676647082672_5.95080784466231,682.461_y6:null_null_null," "79.42:5.6,79.54:224.1,79.59:448.2,79.76:224.1,79.88:12.9" 79.62 79.54 98 2.2e+11 0.05 0.05 0.05 0.075 0.05 0.05 0.13 0.075 0.83 0.5 0.05 1 1 1 "79.6701410827928_79.5354174144454_79.6240287429621_79.6483166666667_79.5910666666667_N/A" 79.3525458229509 "90_97.6219697496854_88.7463292320892_91_72.4676647082672_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.243758544421155_0.528428748833363_0.252555047733111_0.0799652972863214_0.076932157665965_N/A" "5.66958929140032_4.57339987647979_5.71095956606776_5.95762734469545_5.95080784466231_N/A" "1_1_1_1_2_N/A" "611.418113158727_N/A_713.400590977468_600.322472828647_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "20.3333333333333_N/A_13.3333333333333_13.3333333333333_N/A_N/A" "0.00468367310111262_N/A_0.0414710329371246_0.0432300631625822_N/A_N/A" "0_0_1_1_0_0" "1_1_1_1_1_1" "Unknown_Unknown_True_True_Unknown_Unknown" "True_True_True_True_True_False" "0_0_385.256450887155_0_611.418113158727_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.2433156865484 -0.623315686548437 +"15:39:10" 1 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:57015.9032730408_3179.28802151898_34.5062572331775,682.461_y6:26547.8533866248_1531.53349058906_10.1540308260467,813.5015_y7:null_null_null,927.5444_y8:4710.14571196128_311.046685958132_23.7671628541292,826.4855_b8:5623.87054918893_485.363560547921_29.2921895090756,713.4014_b7:4968.18006465682_402.277941635504_47.7510039603103," "79.38:446.9,79.61:3202.7,79.78:6405.4,79.84:3202.7,79.95:516.6" 79.74 79.75 3200 2e+11 0.04 0.099 0.054 0.074 0.079 0.05 0.03 0.05 0.96 0.5 0.11 19 3 1 "79.7538373722019_79.7293599802324_N/A_79.671285566448_79.7388333575673_79.7769170027905" 79.3516493884757 "3179.28802151898_1531.53349058906_N/A_311.046685958132_485.363560547921_402.277941635504" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.335977407753276_0.227270600175473_N/A_0.26323496889087_0.127107804290631_0.225343354901668" "34.5062572331775_10.1540308260467_N/A_23.7671628541292_29.2921895090756_47.7510039603103" "3_1_N/A_3_3_5" "984.534684514473_682.462535513611_813.512211224397_927.558700957285_826.491007832543_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "69.3333333333333_151.666666666667_51.3333333333333_33.6666666666667_34.3333333333333_N/A" "0.0232913063407523_0.0484521503117321_0.0528403844602963_0.0372070591787406_0.011611557602123_N/A" "1_1_1_0_0_0" "1_1_1_1_1_1" "True_True_True_Unknown_Unknown_Unknown" "True_True_False_True_True_True" "0_0_385.259700124044_498.343092902756_611.425227124944_682.462535513611_813.512211224397_927.558700957285_984.534684514473_1097.63287202846_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3699472702056 -0.629947270205562 +"15:39:10" 2 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:30225.8937522149_1578.76916894474_27.7677453844382,713.4014_b7:null_null_null," "78.23:84.3,78.5:837.8,78.75:1675.6,78.86:837.8,79.26:109.4" 78.72 78.71 1600 680000 0.5 0.5 0.75 0.079 0.5 0.75 0.29 0.49 0.005 0.5 0.75 19 3 3 "78.6972657502929_N/A_N/A_78.7246723666666_78.710089674726_N/A" 79.3516493884757 "8552.38452203284_N/A_N/A_1156.23139827393_1578.76916894474_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.345281234297929_N/A_N/A_0.212948211561695_0.364075487293974_N/A" "33.5613071852383_N/A_N/A_20.3437924072273_27.7677453844382_N/A" "1_N/A_N/A_1_1_N/A" "984.581835479902_682.422470048131_N/A_927.559966067391_826.490992297568_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "808.333333333333_30.6666666666667_N/A_104.666666666667_136_N/A" "0.0564204975522671_0.0107670058432632_N/A_0.0539109831117912_0.0382135553466014_N/A" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_False_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.121945199736_288.155893868708_385.191182750177_498.315041890289_0_682.398807140688_0_927.46721133992_0_1097.5832007727_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.3075423860607 -0.587542386060747 +"15:39:10" 3 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:2983.34258884189_204.233382842502_26.6140968851804,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:1097.63001565599_96.1437667326109_29.0428178025378,713.4014_b7:null_null_null," "75.28:166.9,75.37:223.8,75.51:447.6,75.59:223.8,75.71:128.1" 75.48 75.5 200 300 0.5 0.5 0.75 0.5 0.5 0.75 0.79 0.76 0.41 0.5 0.75 19 3 2 "75.4965974403081_75.4808681471833_N/A_N/A_75.4739254353535_N/A" 79.3516493884757 "204.233382842502_113.737738289296_N/A_N/A_96.1437667326109_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.236583966499282_0.236357229187504_N/A_N/A_0.207585875881321_N/A" "26.6140968851804_9.84331227136362_N/A_N/A_29.0428178025378_N/A" "6_4_N/A_N/A_17_N/A" "984.55870899699_682.485838605534_N/A_927.482983309254_N/A_713.391664896205" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "13.6666666666667_13.3333333333721_N/A_13.6666666666279_N/A_40.9999999995343" "0.0268199630233994_0.00491664653850421_N/A_0.0188067448916627_N/A_0.00436698871874341" "1_2_0_2_0_2" "1_1_1_1_1_1" "True_False_Unknown_False_Unknown_False" "True_True_False_False_True_False" "0_288.107964759873_385.172450640585_0_0_0_0_0_984.55870899699_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.7407228994736 -0.26072289947362
--- a/tool_dependencies.xml Thu May 21 12:47:52 2015 -0400 +++ b/tool_dependencies.xml Sat May 30 05:27:37 2015 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7"> - <repository changeset_revision="25b20b323706" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="92611fea803c" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="msproteomicstools" version="0.3.2"> <repository changeset_revision="4381e493affd" name="package_python_2_7_msproteomicstools_0_3_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />