1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
|
//
// File: test_timsframe.cpp
// Created by: Olivier Langella
// Created on: 12/4/2020
//
/*******************************************************************************
* Copyright (c) 2020 Olivier Langella <olivier.langella@u-psud.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/>.
*
******************************************************************************/
// make test ARGS="-V -I 1,1"
// ./tests/pappsotree/catch2-only-pappsotree [cubicsolver] -s
// ./tests/pappsotree/catch2-only-pappsotree [timsframe] -s -a
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <QCoreApplication>
#include <QDebug>
#include <QString>
#include <iostream>
#include <pappsomspp/core/vendors/tims/timsframebase.h>
#include <pappsomspp/core/vendors/tims/mzcalibration/cardano.h>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/private/timsmsrunreaderms2.h>
#include <pappsomspp/core/msrun/private/timsmsrunreader.h>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/processing/filters/filtersuitestring.h>
#include <pappsomspp/core/processing/filters/filterresample.h>
#include "tests/tests-config.h"
using namespace pappso;
using namespace std;
TEST_CASE("Test Cardano's cubic solver", "[cubicsolver]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("Test TIMS TDF parsing issue #61")
{
INFO("Test case ERROR reading TIMS frame 58581");
// QApplication app(QString(), QString());
int argc(0);
char *argv[] = {};
QCoreApplication *app [[maybe_unused]] = new QCoreApplication(argc, argv);
pappso::MsFileAccessor accessor(
"/gorgone/pappso/versions_logiciels_pappso/bruker/"
"200ngHeLaPASEF_2min_compressed.d",
"a1");
INFO("setPreferredFileReaderType");
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
INFO(" accessor.msRunReaderSPtr");
pappso::MsRunReaderSPtr p_msreader = accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
REQUIRE(p_msreader != nullptr);
REQUIRE(accessor.getFileReaderType() == Enums::FileReaderType::tims_ms2);
pappso::TimsMsRunReaderMs2 *tims2_reader =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_msreader.get());
REQUIRE(tims2_reader != nullptr);
if(tims2_reader != nullptr)
{
tims2_reader->setMs2BuiltinCentroid(true);
tims2_reader->setMs2FilterCstSPtr(std::make_shared<FilterSuiteString>(""));
}
pappso::QualifiedMassSpectrum mass_spectrum;
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(5001));
/*
REQUIRE(
mass_spectrum.getMassSpectrumCstSPtr().get()->toString().toStdString()
==
"");
*/
Trace filter_trace(*mass_spectrum.getMassSpectrumCstSPtr().get());
// REQUIRE(filter_trace.toString().toStdString() == "");
QFile f(QString(CMAKE_SOURCE_DIR).append("/tests/data/timstof/ms2_5001.tsv"));
REQUIRE(f.open(QFile::ReadOnly | QFile::Text));
QTextStream in(&f);
Trace control_trace(in.readAll());
REQUIRE_THAT(filter_trace.xValues(), Catch::Matchers::Approx(control_trace.xValues()));
REQUIRE_THAT(filter_trace.yValues(), Catch::Matchers::Approx(control_trace.yValues()));
// 2762 => 2291
// 2762 => 2322
REQUIRE(filter_trace.size() == 2322);
REQUIRE(filter_trace.sumY() == Catch::Approx(289706.9697384664));
FilterResampleKeepXRange(1075, 1078).filter(filter_trace);
REQUIRE_THAT(filter_trace.xValues(),
Catch::Matchers::Approx(std::vector<double>({1075.5218269238,
1075.53223643,
1075.5426460307,
1076.0996328182,
1076.2922693084,
1076.5057514656,
1076.5317873147,
1076.5526162383,
1076.833826252,
1077.521383186})));
REQUIRE_THAT(filter_trace.yValues(),
Catch::Matchers::Approx(std::vector<double>({168.423935369,
131.4528276051,
54.7720115021,
15.0623031631,
43.8176092017,
71.2036149528,
246.4740517596,
83.5273175407,
15.0623031631,
86.2659181158})));
FilterResampleKeepXRange(1531, 1964).filter(filter_trace);
REQUIRE_THAT(filter_trace.xValues(), Catch::Matchers::Approx(std::vector<double>({})));
REQUIRE_THAT(filter_trace.yValues(), Catch::Matchers::Approx(std::vector<double>({})));
filter_trace = (*mass_spectrum.getMassSpectrumCstSPtr().get());
FilterResampleKeepXRange(105, 188).filter(filter_trace);
REQUIRE_THAT(filter_trace.xValues(),
Catch::Matchers::Approx(std::vector<double>({105.2508651592,
122.7051378682,
133.6175290647,
172.8936930658,
183.2788453809,
186.0653089587,
186.7109907881,
187.021228504,
187.1406192812,
187.1449614799})));
REQUIRE_THAT(filter_trace.yValues(),
Catch::Matchers::Approx(std::vector<double>({15.0623031631,
15.0623031631,
13.6930028755,
36.9711077639,
13.6930028755,
15.0623031631,
31.4939066137,
71.2036149528,
119.1291250171,
105.4361221416})));
/*
* 23: ..:: Test TIMS frame init begin ::..
23: Test case ERROR reading TIMS frame 58581
23: ERROR reading TIMS frame 60575 TIMS binary file
/home/langella/data1/bruker/ 23:
5-18-2021_1_robert_28_mic02-std_1354.d/analysis.tdf_bin: decompressed_size2 23:
== ZSTD_CONTENTSIZE_ERROR, frame_length=265254592
*/
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6001));
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6003));
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6005));
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(6007));
REQUIRE_THROWS_AS(mass_spectrum = tims2_reader->qualifiedMassSpectrum(35460),
pappso::ExceptionNotFound);
REQUIRE_NOTHROW(mass_spectrum = tims2_reader->qualifiedMassSpectrum(5001));
filter_trace = *mass_spectrum.getMassSpectrumCstSPtr().get();
REQUIRE_THAT(filter_trace.xValues(), Catch::Matchers::Approx(control_trace.xValues()));
REQUIRE_THAT(filter_trace.yValues(), Catch::Matchers::Approx(control_trace.yValues()));
}
SECTION("Test TIMS TDF parsing")
{
INFO("Test case Enums::FileReaderType::tims_ms2 start");
pappso::MsFileAccessor accessor(
"/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/"
"PXD014777_maxquant_timstof/"
"20180809_120min_200ms_WEHI25_brute20k_timsON_100ng_HYE124B_Slot1-8_1_"
"894.d/analysis.tdf",
"a1");
/*
pappso::MsFileAccessor accessor(
"/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/"
"example_data/200ngHeLaPASEF_2min_compressed.d/"
"analysis.tdf",
"a1");
*/
/*
pappso::MsFileAccessor accessor(
"/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/"
"example_data/"
"200ngHeLaPASEF_2min_compressed.d/analysis.tdf",
"a1");
*/
/*
pappso::MsFileAccessor accessor(
"/data/test_tdf_quality/2-3-2021_1_HeLa10ng_871.d/analysis.tdf",
"a1");
*/
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims);
pappso::MsRunReaderSPtr p_msreader_tims_ms1 =
accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
pappso::TimsMsRunReader *tims1_reader =
dynamic_cast<pappso::TimsMsRunReader *>(p_msreader_tims_ms1.get());
REQUIRE_FALSE(p_msreader_tims_ms1.get() == nullptr);
REQUIRE_FALSE(tims1_reader == nullptr);
pappso::TimsDataSp timsdata_sp = tims1_reader->getTimsDataSPtr();
REQUIRE_NOTHROW(timsdata_sp.get()->getScanByGlobalScanIndex(0));
REQUIRE_NOTHROW(timsdata_sp.get()->getScanByGlobalScanIndex(1));
REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(0));
// REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(1000));
for(std::size_t i = 0; i < 1000; i++)
{
qDebug() << " size(" << (i)
<< ")=" << p_msreader_tims_ms1.get()->massSpectrumCstSPtr(i).get()->size();
}
p_msreader_tims_ms1.get()->massSpectrumCstSPtr(53);
p_msreader_tims_ms1.get()->massSpectrumCstSPtr(5000);
// timsdata_sp.get()->getRawMsBySpectrumIndex(8207);
REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(8207));
// 8206, frameId=9 scanNum=910 ERROR in
// MzCalibrationModel1::getMzFromTofIndex m[0].y!= 0
REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(8206));
// scan_num=899 spectrum_index=899
REQUIRE_NOTHROW(p_msreader_tims_ms1.get()->massSpectrumCstSPtr(899));
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_msreader = accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
REQUIRE(p_msreader != nullptr);
REQUIRE(accessor.getFileReaderType() == Enums::FileReaderType::tims_ms2);
pappso::TimsMsRunReaderMs2 *tims2_reader =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_msreader.get());
REQUIRE(tims2_reader != nullptr);
if(tims2_reader != nullptr)
{
tims2_reader->setMs2BuiltinCentroid(true);
tims2_reader->setMs2FilterCstSPtr(
std::make_shared<FilterSuiteString>(FilterSuiteString("chargeDeconvolution|0.02dalton")));
}
pappso::QualifiedMassSpectrum mass_spectrum = tims2_reader->qualifiedMassSpectrum(7001);
INFO("mass_spectrum.getMsLevel()=" << mass_spectrum.getMsLevel());
INFO("mass_spectrum.getPrecursorMz()=" << mass_spectrum.getPrecursorMz());
INFO("mass_spectrum.getMassSpectrumId().getSpectrumIndex()="
<< mass_spectrum.getMassSpectrumId().getSpectrumIndex());
INFO(mass_spectrum.getMassSpectrumSPtr()->xValues().at(0));
REQUIRE_FALSE(mass_spectrum.getMassSpectrumCstSPtr().get()->back().x < 40.0);
INFO("Test case Enums::FileReaderType::tims start");
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims);
class SpectrumCollectionHandler : public SpectrumCollectionHandlerInterface
{
public:
virtual ~SpectrumCollectionHandler() {};
virtual void
setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override
{
m_count++;
if((m_count % 1000) == 0)
{
WARN("count " << m_count << " "
<< spectrum.getMassSpectrumId().getNativeId().toStdString()
<< " MSlevel=" << spectrum.getMsLevel());
if(spectrum.getMsLevel() == 1)
{
REQUIRE_FALSE(spectrum.getMassSpectrumCstSPtr() == nullptr);
}
if(spectrum.getMassSpectrumCstSPtr() != nullptr)
{
WARN(" size=" << spectrum.size());
}
//<< " size=" << spectrum.toString().toStdString());
}
};
virtual bool
needPeakList() const override
{
return false;
};
std::size_t m_count = 0;
};
SpectrumCollectionHandler dummy_handler;
Catch::Timer t;
t.start();
WARN("reading all spectrum collection of file " << accessor.getFileName().toStdString());
dummy_handler.setNeedMsLevelPeakList(1, false);
dummy_handler.setNeedMsLevelPeakList(2, false);
// tims1_reader->readSpectrumCollectionByMsLevel(dummy_handler, 1);
auto s = t.getElapsedSeconds();
WARN("reading time in second : " << s);
// git hash 597d6a68062a45d5e3ccaaa8398598a62dc69043 reading time in second
// : 1447.15
// git hash 7dc0806a4ca1fd0e92da97dcc44ac9b44c381d9f reading time in second
// : 1445.65
// if we disable binary data reading : reading time in second : 1220.77 =>
// there is somehow room for performance enhancements
// git hash 26c8053d4fcfae15b98c75b715d79cd615bf42e0 reading time in second
// : 1440.25
// git hash 2d0d2a4edcfcef583bc60bd5b14e6b0df1505a02 reading time in second
// : 1447.3
// => avoiding sql query is not really efficient
}
/*
std::cout << std::endl
<< mass_spectrum.getMassSpectrumCstSPtr()
.get()
->toString()
.toStdString()
.c_str()
<< std::endl;
*/
/*
*
22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@513,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid():
375176 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@518,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid():
99944.2 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@253,
pappso::TimsFrameBase::getMzFromTof(): m.length()= 3 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@520,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid(): 41.3832
polynome :
-101811 2523.58 -0.002221 313.267
=> m1= 42.058
*/
/*
22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@513,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid():
374144 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@518,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid():
99692.8 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@192,
pappso::TimsFrameBase::getMzFromTof(): 0 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@253,
pappso::TimsFrameBase::getMzFromTof(): m.length()= 2 22:
/home/langella/developpement/git/pappsomspp/src/pappsomspp/vendors/tims/timsframebase.cpp@520,
pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid():
1554.74
polynome :
-100327 2520.37 0.000338744
=> m1= 1584.54
*/
}
|
