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
|
// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow, Hendrik Weisser $
// $Authors: Chris Bielow, Hendrik Weisser $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/FORMAT/PepXMLFile.h>
///////////////////////////
#include <OpenMS/CONCEPT/FuzzyStringComparator.h>
#include <OpenMS/FORMAT/MzMLFile.h>
using namespace OpenMS;
using namespace std;
START_TEST(PepXMLFile, "$Id: PepXMLFile_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PepXMLFile* ptr = 0;
PepXMLFile* nullPointer = 0;
PepXMLFile file;
START_SECTION(PepXMLFile())
ptr = new PepXMLFile();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PepXMLFile())
delete ptr;
END_SECTION
START_SECTION(void load(const String &filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides, const String& experiment_name, const MSExperiment<>& experiment, bool use_precursor_data = false))
{
vector<ProteinIdentification> proteins, proteins2;
vector<PeptideIdentification> peptides, peptides2;
String pep_file = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test.pepxml");
String mz_file = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test.mzML");
String exp_name = "PepXMLFile_test";
MSExperiment<> experiment;
MzMLFile().load(mz_file, experiment);
// load with precursor information:
file.load(pep_file, proteins, peptides, exp_name, experiment, true);
PeptideIdentification first = peptides[0];
TEST_EQUAL(first.getMetaValue("RT"), 0.5927);
TEST_EQUAL(first.getMetaValue("MZ"), 538.605);
// load without precursor information (tested more thoroughly below):
file.load(pep_file, proteins2, peptides2);
TEST_EQUAL(peptides.size(), peptides2.size());
TEST_EQUAL(proteins.size(), proteins2.size());
// check that only m/z and RT differ between "load" methods:
for (Size i = 0; i < peptides.size(); ++i)
{
peptides[i].clearMetaInfo();
peptides2[i].clearMetaInfo();
}
TEST_EQUAL(peptides == peptides2, true);
TEST_EQUAL(proteins == proteins2, true);
}
END_SECTION
START_SECTION(void load(const String& filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides, const String& experiment_name = ""))
{
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
// file contains results from two search runs:
String filename = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test.pepxml");
String exp_name = "PepXMLFile_test";
file.load(filename, proteins, peptides, exp_name);
// peptide IDs:
TEST_EQUAL(peptides.size(), 18);
PeptideIdentification first = peptides.front(), last = peptides.back();
bool accu_result = true; // to avoid spamming TEST_EQUAL's in the "for" loop
for (Size i = 1; i < 9; ++i)
{ // should be the same for all peptides from the first search run:
accu_result &= (first.getIdentifier() == peptides[i].getIdentifier());
accu_result &= (first.getScoreType() == peptides[i].getScoreType());
accu_result &= (first.isHigherScoreBetter() ==
peptides[i].isHigherScoreBetter());
accu_result &= (first.getSignificanceThreshold() ==
peptides[i].getSignificanceThreshold());
}
TEST_EQUAL(accu_result, true);
TEST_EQUAL(first.getMetaValue("RT"), 1.3653); // RT of MS2 spectrum
TEST_REAL_SIMILAR(first.getMetaValue("MZ"), 538.605); // recomputed
TEST_EQUAL(first.getHits().size(), 1);
PeptideHit pep_hit = first.getHits()[0];
TEST_EQUAL(pep_hit.getSequence().toString(), "(Glu->pyro-Glu)ELNKEMAAEKAKAAAG");
TEST_EQUAL(pep_hit.getSequence().toUnmodifiedString(), "ELNKEMAAEKAKAAAG");
TEST_EQUAL(pep_hit.getRank(), 1);
// no use checking score, because implementation may still change
TEST_EQUAL(pep_hit.getCharge(), 3);
TEST_EQUAL(pep_hit.getProteinAccessions().size(), 3);
TEST_EQUAL(pep_hit.getProteinAccessions()[0], "ddb000449223");
TEST_EQUAL(pep_hit.getAABefore(), 'R');
TEST_EQUAL(pep_hit.getAAAfter(), 'E');
TEST_EQUAL(first.getHits()[0].getSequence().isModified(), true);
TEST_EQUAL(first.getHits()[0].getSequence().hasNTerminalModification(), true);
TEST_EQUAL(first.getHits()[0].getSequence().hasCTerminalModification(),
false);
TEST_EQUAL(peptides[1].getHits()[0].getSequence().isModified(), true);
TEST_EQUAL(peptides[1].getHits()[0].getSequence().hasNTerminalModification(), true);
TEST_EQUAL(peptides[1].getHits()[0].getSequence().hasCTerminalModification(), false);
TEST_EQUAL(peptides[5].getHits()[0].getSequence().isModified(), true);
TEST_EQUAL(peptides[5].getHits()[0].getSequence().hasNTerminalModification(), false);
TEST_EQUAL(peptides[5].getHits()[0].getSequence().hasCTerminalModification(), false);
// cursory check of a peptide ID from the second search run:
pep_hit = last.getHits()[0];
TEST_EQUAL(pep_hit.getSequence().toString(), "EISPDTTLLDLQNNDISELR");
// protein ID:
TEST_EQUAL(proteins.size(), 2);
TEST_EQUAL(proteins[0].getIdentifier(), first.getIdentifier());
TEST_EQUAL(proteins[1].getIdentifier(), last.getIdentifier());
TEST_NOT_EQUAL(proteins[0].getIdentifier(), "");
TEST_NOT_EQUAL(proteins[1].getIdentifier(), "");
TEST_NOT_EQUAL(proteins[0].getIdentifier(), proteins[1].getIdentifier());
TEST_EQUAL(proteins[0].getSearchEngine(), "X! Tandem (k-score)");
TEST_EQUAL(proteins[1].getSearchEngine(), "SEQUEST");
vector<ProteinHit> prot_hits = proteins[0].getHits();
TEST_EQUAL(prot_hits.size(), 20);
StringList accessions;
for (std::vector<ProteinHit>::iterator it = prot_hits.begin();
it != prot_hits.end(); ++it)
{
accessions << it->getAccession();
}
// check a sample of the IDs that should be present:
TEST_EQUAL(accessions.contains("ddb000449223"), true);
TEST_EQUAL(accessions.contains("ddb000626346"), true);
TEST_EQUAL(accessions.contains("rev000409159"), true);
// search parameters:
ProteinIdentification::SearchParameters params = proteins[0].getSearchParameters();
TEST_EQUAL(params.db, "./current.fasta");
TEST_EQUAL(params.mass_type, ProteinIdentification::MONOISOTOPIC);
TEST_EQUAL(params.enzyme, ProteinIdentification::TRYPSIN);
vector<String> fix_mods(params.fixed_modifications), var_mods(params.variable_modifications);
TEST_EQUAL(fix_mods.size(), 1)
TEST_EQUAL(var_mods.size(), 4)
TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "C-17.0265") != var_mods.end(), true)
TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "E-18.0106") != var_mods.end(), true)
TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "M+15.9949") != var_mods.end(), true)
TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "Q-17.0265") != var_mods.end(), true)
//TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "Carbamidometyhl (C)") != var_mods.end(), true)
//TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "Gln->pyro-Glu (Q)") != var_mods.end(), true)
//TEST_EQUAL(find(var_mods.begin(), var_mods.end(), "Glu->pyro-Glu (E)") != var_mods.end(), true)
// wrong "experiment_name" produces an exception:
TEST_EXCEPTION(Exception::ParseError, file.load(filename, proteins, peptides, "abcxyz"));
// throw an exception if the pepXML file does not exist:
TEST_EXCEPTION(Exception::FileNotFound, file.load("this_file_does_not_exist_but_should_be_a_pepXML_file.pepXML", proteins, peptides, exp_name));
}
END_SECTION
START_SECTION(void store(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids))
{
PepXMLFile file;
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
String filename = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test_store.pepxml");
file.load(filename, proteins, peptides);
String cm_file_out;
NEW_TMP_FILE(cm_file_out);
file.store(cm_file_out, proteins, peptides);
FuzzyStringComparator fsc;
fsc.setWhitelist (StringList::create("base_name"));
String filename_out = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test_out.pepxml");
TEST_EQUAL(fsc.compareFiles (cm_file_out.c_str(), filename_out.c_str()), true)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
