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//
// File: test_c13n15.cpp
// Created by: Olivier Langella
// Created on: 12/7/2023
//
/*******************************************************************************
* Copyright (c) 2023 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
// ./tests/dia/catch2-only-dia [soleil] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <pappsomspp/core/vendors/tims/timsframe.h>
#include <pappsomspp/core/msrun/private/timsmsrunreaderms2.h>
#include <pappsomspp/core/msrun/private/timsmsrunreader.h>
#include <QDebug>
#include "../common.h"
#include "tests/tests-config.h"
#include "dia_lib.h"
TEST_CASE("soleil test suite.", "[soleil]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("Test TIMS TDF parsing DIA")
{
INFO("Test case mobility trace extractor");
pappso::MsFileAccessor dia_accessor(
"/gorgone/pappso/jouy/raw/2023_TimsTOF_Pro/20231006_Guillaume_Test_DIA3/"
"DIA/10-5-2023_AT01_20ng_DIA3_1_6490.d",
"a1");
dia_accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims);
pappso::MsRunReaderSPtr p_ms_data_file =
dia_accessor.msRunReaderSPtr(dia_accessor.getMsRunIds().front());
pappso::TimsMsRunReader *p_msreader_tims_ms =
dynamic_cast<pappso::TimsMsRunReader *>(p_ms_data_file.get());
/*
E:\Guillaume_S\10-05-2023_Test_DIA3\10-5-2023_AT01_20ng_DIA3_1_6490.d
10-5-2023_AT01_20ng_DIA3_1_6490 AT3G20410.1;AT3G20410.2
AT3G20410.1;AT3G20410.2 | | 186,004 639,495 843,356 3494850 13979800
6624770 6624770 AAAAAPGLSPK AAAAAPGLSPK AAAAAPGLSPK2 2 0,00439932
0,0805417 0,00222608 0,333333 0,0191446 0,000202963 0,333333 0 1 186,004
639,495 150,324 206,898 0,678122 18,7117 18,6216 18,8019 -10,6384
18,6526 -10,4488 0,00317137 0,000236798 0,490145 256,006 1,83272
0,330662 0,086652 0 0,945514 0
-10000000 71.0021;0;115.002;0;134.003;0;0;0;0;0;0;0; 71.0021;0;115.002;0;134.003;0;0;0;0;0;0;0;
0.628757;0;0.708601;0;0.940796;0;0;0;0;0;0;0; 19916 0,852614 0,866875
0,850309 0,869149
*/
/*
E:\Guillaume_S\10-05-2023_Test_DIA3\10-5-2023_AT01_20ng_DIA3_1_6490.d
10-5-2023_AT01_20ng_DIA3_1_6490 AT1G13060.1 AT1G13060.1;AT1G13060.2;AT1G13060.3
| | 4426,15 16651,3 14524,4 3494850 13979800 6624770 6624770 GGVMVAADSR
GGVMVAADSR GGVMVAADSR2 2 0,0000591509 0,0000591509 0,0000236407 0,333333
0,000270929 0,000202963 0,333333 0 1 3169,08 10895,5 2561,17 11503,5 0,948014
18,7124 18,6223 18,8026 -11,0752 18,7199 -11,0749 0,00000383822 0,000236798
0,937327 9936,22 4,89793 0,289596 0,993191 1,64454 0,999998 0,889416
0,0101333 4868.11;2112.05;859.021;611.016;543.012;889.022;
4868.11;2112.05;859.021;611.016;543.012;889.022;
0.863006;0.982854;0.900798;0.840894;0.839806;0.910868; 19916 0,834792 0,834792
0,832547 0,83742
*/
/*
E:\Guillaume_S\10-05-2023_Test_DIA3\10-5-2023_AT01_20ng_DIA3_1_6490.d
10-5-2023_AT01_20ng_DIA3_1_6490 AT3G04840.1 AT3G04840.1 | | 42216 161027
152055 3494850 13979800 6624770 6624770 TTDSYTLR TTDSYTLR TTDSYTLR2 2
0,00000841411 0,00000841411 0,0000859555 0,333333 0,000270929 0,000202963
0,333333 0 1 9335,2 32095 7544,48 137159 0,937962 18,7137 18,6235
18,8038 -11,4401 18,694 -11,413 0,00000179435 0,000236798 0,988696
142929 5,42457 0,672722 1 1,67381 1 0 -10000000
23852.4;17278.4;19233.4;3404.05;796.02;570.011;
23852.4;17278.4;19233.4;3404.05;796.02;570.011;
0.918867;0.956514;0.944977;0.922522;0.808919;0.970996; 19916 0,8 0,788977
0,787844 0,801915
*/
// scan 19916
// AAAAAPGLSPK
// mass 952.534180433232
// mz 477.274
// rt 18,7117
// GGVMVAADSR mz 481.7398
// TTDSYTLR mz 478.7378
// "global_slice_index=19917 frame=10581 begin=632 end=926 group=6 slice=1"
// "frame_id=10575 begin=632 end=926 group=6 slice=1"
pappso::TimsFrameCstSPtr timsframe_sptr;
timsframe_sptr =
p_msreader_tims_ms->getTimsDataSPtr().get()->getTimsFrameCstSPtr(10581);
pappso::TimsFrameMobilityTraces tims_frame_mobility_traces;
tims_frame_mobility_traces.extractMobilityTraces(
timsframe_sptr, 632, 926, 1000);
writeMobilityTraces("mobility_dia_nano_10581_ms2",
tims_frame_mobility_traces);
timsframe_sptr =
p_msreader_tims_ms->getTimsDataSPtr().get()->getTimsFrameCstSPtr(10575);
tims_frame_mobility_traces.extractMobilityTraces(
timsframe_sptr, 632, 926, 1000);
writeMobilityTraces("mobility_dia_nano_10575_ms1",
tims_frame_mobility_traces);
timsframe_sptr =
p_msreader_tims_ms->getTimsDataSPtr().get()->getTimsFrameCstSPtr(13338);
tims_frame_mobility_traces.extractMobilityTraces(
timsframe_sptr, 552, 877, 1000);
writeMobilityTraces("mobility_dia_nano_13338_ms2",
tims_frame_mobility_traces);
timsframe_sptr =
p_msreader_tims_ms->getTimsDataSPtr().get()->getTimsFrameCstSPtr(13329);
tims_frame_mobility_traces.extractMobilityTraces(
timsframe_sptr, 552, 877, 1000);
writeMobilityTraces("mobility_dia_nano_13329_ms1",
tims_frame_mobility_traces);
}
SECTION("Test TIMS TDF parsing")
{
INFO("Test case mobility trace extractor");
pappso::MsFileAccessor accessor(
"/gorgone/pappso/versions_logiciels_pappso/bruker/"
"200ngHeLaPASEF_2min_compressed.d/analysis.tdf",
"a1");
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_ms_data_file =
accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
pappso::TimsMsRunReaderMs2 *p_msreader_tims_ms2 =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_ms_data_file.get());
/*
* 36 1101.0713085818 1101.2352981594 1100.56987430806 2 206.34670754313
27481.0 7
37 1032.50460066644 1032.61931820008 1032.00354342756 2
255.636031950547 7776.0 7
38 849.889511073675 850.36577904552
849.889511073675 2 301.081436858545 10674.0 7
39 732.368888386124
732.7994188422 732.368888386124 2 366.846506680738 171577.0 7
40 613.834985672256 614.145093980785 613.834985672256 2 408.353586866372
100182.0 7
41 590.663111414989 590.993423163968 590.663111414989 3
480.650093737275 11285.0 7
42 1186.54230445333 1186.72886658555
1186.04087739917 2 209.745072692947 3388.0 7
43 675.889879111058
676.29815138184 675.889879111058 2 357.036750108284 78563.0 7
44
625.325372791376 625.579928168419 625.325372791376 1 408.432368202426
103456.0 7
45 1007.51213556948 1007.6267841152 1007.01070658348 2
247.074788254945 7187.0 7
46 913.959890656205 913.979678622373
913.458905261467 2 294.654254399024 8314.0 7 47 755.38529656205
755.841674769364 755.38529656205 2 353.86257989541 12945.0 7
48
591.302490003786 591.590497194694 591.302490003786 2 403.254182106694
29830.0 7
49 595.771231095101 596.059238283215 595.771231095101 2
446.612758885196 9435.0 7
50 413.752273442763 413.939477660886
413.752273442763 1 509.25342989311 6639.0 7 51 762.399893323618
762.856367409854 762.399893323618 2 322.644976866487 8675.0 7 52
735.843048722056 736.273579192029 735.843048722056 2 373.54662077597 18891.0
7 53 568.32624886187 568.614256051375 568.32624886187 2 429.363085740713
10674.0 7 54 643.816041172731 644.126137985901 643.816041172731 2
399.427994121969 15462.0 7 55 687.390246797748 687.798519066724
687.390246797748 2 363.680236411293 11928.0 7 56 562.806530794766
563.094537974134 562.806530794766 2 405.175837742504 13135.0 7 57
546.269682718966 546.539497651969 546.269682718966 2 450.784556792487 7570.0
7 58 509.960123743293 510.26725044115 509.960123743293 3 496.035031847134
6328.0 7 59 883.463248838573 883.962935681494 883.463248838573 2
225.932830827769 5538.0 7 60 938.950034464637 938.969822427669
938.4490490699 2 300.353033535402 7770.0 7 61 729.330713601629
729.761244061435 729.330713601629 2 378.503772398617 10847.0 7 62
578.827527999194 579.115535190246 578.827527999194 2 418.782881695176 8674.0
7 63 497.283111759912 497.529947222637 497.283111759912 2 467.090705461384
7569.0 7 64 417.732442590361 417.732442590361 514.431244560487 3550.0
7 65 874.942898591935 875.442503475723 874.942898591935 2 305.569882347679
6660.0 7 66 751.906613734472 752.363087819094 751.906613734472 2
352.740672716387 9542.0 7 67 791.370289287521 791.490672694711
791.036000584609 3 396.117318241086 8795.0 7 68 455.606517405094
455.889596549243 455.606517405094 3 497.462564102564 5917.0 7
* */
pappso::TimsFrameCstSPtr timsframe_sptr;
timsframe_sptr =
p_msreader_tims_ms2->getTimsDataSPtr().get()->getTimsFrameCstSPtr(13);
// LVSNHSLHETSSVFVDSLTK 71
// prec 36 1101.0713085818 1101.2352981594 1100.56987430806 2
// 206.34670754313 27481.0 7
// frameprec 13 194 219 1101.2352981594 3.0 68.0 36
/*
*
<peptide id="pd3148" seq="LVSNHSLHETSSVFVDSLTK"/>
<peptide_evidence id="peb34" peptide_id="pd3148" idx="71"
rt="2402.244825" eng="1" evalue="2.25835e-09" exp_mass="2199.125195"
charge="2" checked="true"> <param key="0" value="44.2"/> <param key="1"
value="2.25835e-09"/>
</peptide_evidence>*/
// AWGPGLEGGVVGK 79
// prec 40 613.834985672256 614.145093980785 613.834985672256 2
// 408.353586866372 100182.0 7
// frameprec 13 396 421 614.145093980785 2.0 42.0 40
/*
*
<peptide id="pd1376" seq="AWGPGLEGGVVGK"/>
<peptide_evidence id="peb38" peptide_id="pd1376" idx="79"
rt="2402.244825" eng="1" evalue="3.55081e-06" exp_mass="1225.655418"
charge="2" checked="true"> <param key="0" value="42"/> <param key="1"
value="3.55081e-06"/>
</peptide_evidence>*/
// AVEGC[MOD:00397]VSASQAATEDGQLLR 73
// prec 37 1032.50460066644 1032.61931820008 1032.00354342756 2
// 255.636031950547 7776.0 7
// frameprec 13 243 268 1032.61931820008 3.0 58.0 37
// 14 243 268 1032.61931820008 3.0 58.0 37
// 16 243 268 1032.61931820008 3.0 58.0 37
/*
*
<peptide id="pd1946" seq="AVEGCVSASQAATEDGQLLR">
<mod ref="moda6" position="4" aa="C"/>
</peptide>
<peptide_evidence id="peb35" peptide_id="pd1946" idx="73"
rt="2402.244825" eng="1" evalue="1.25003e-08" exp_mass="2061.992533"
charge="2" checked="true"> <param key="0" value="38.8"/> <param key="1"
value="1.25003e-08"/>
</peptide_evidence>*/
/*
<peptide_evidence id="peb34" peptide_id="pd3148" idx="71"
rt="2402.244825" eng="1" evalue="2.25835e-09" exp_mass="2199.125195"
charge="2" checked="true"> <param key="0" value="44.2"/> <param key="1"
value="2.25835e-09"/><peptide id="pd3148" seq="LVSNHSLHETSSVFVDSLTK"/>
</peptide_evidence>
<peptide_evidence id="peb35" peptide_id="pd1946" idx="73"
rt="2402.244825" eng="1" evalue="1.25003e-08" exp_mass="2061.992533"
charge="2" checked="true"> <param key="0" value="38.8"/> <param key="1"
value="1.25003e-08"/><peptide id="pd1946" seq="AVEGCVSASQAATEDGQLLR">
<mod ref="moda6" position="4" aa="C"/>
</peptide>
</peptide_evidence>
<peptide_evidence id="peb36" peptide_id="pd1997" idx="75"
rt="2402.244825" eng="1" evalue="3.33021" exp_mass="1697.764469"
charge="2" checked="true"> <param key="0" value="18.8"/> <param key="1"
value="3.33021"/>
<peptide id="pd1997" seq="NHKDVTDSFYPAMR">
<mod ref="moda7" position="12" aa="M"/>
</peptide>
</peptide_evidence>
<peptide_evidence id="peb37" peptide_id="pd1357" idx="77"
rt="2402.244825" eng="1" evalue="6.40312e-06" exp_mass="1462.723223"
charge="2" checked="true"> <param key="0" value="32.3"/> <param key="1"
value="6.40312e-06"/> <peptide id="pd1357" seq="SPYQEFTDHLVK"/>
</peptide_evidence>
<peptide_evidence id="peb38" peptide_id="pd1376" idx="79"
rt="2402.244825" eng="1" evalue="3.55081e-06" exp_mass="1225.655418"
charge="2" checked="true"> <param key="0" value="42"/> <param key="1"
value="3.55081e-06"/><peptide id="pd1376" seq="AWGPGLEGGVVGK"/>
</peptide_evidence>
<peptide_evidence id="peb39" peptide_id="pd1748" idx="81"
rt="2402.244825" eng="1" evalue="7.82161e-12" exp_mass="1768.967504"
charge="3" checked="true"> <param key="0" value="48"/> <param key="1"
value="7.82161e-12"/><peptide id="pd1748" seq="MEKPPAPPSLPAGPPGVK"/>
*/
pappso::TimsFrameMobilityTraces tims_frame_mobility_traces;
tims_frame_mobility_traces.extractMobilityTraces(
timsframe_sptr,
0,
timsframe_sptr.get()->getTotalNumberOfScans() - 1,
1000);
writeMobilityTraces("mobility_71_73_79", tims_frame_mobility_traces);
}
}
|
