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
|
// --------------------------------------------------------------------------
// 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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVReader.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_ConvertTSVToTraML ConvertTSVToTraML
@brief Converts OpenSWATH transition TSV files to TraML files
The OpenSWATH transition TSV files need to have the following headers, all fields need to be separated by tabs:
<ul>
<li> PrecursorMz (float) </li>
<li> ProductMz (float) </li>
<li> Tr_calibrated (float) </li>
<li> transition_name (free text, needs to be unique for each transition [in this file]) </li>
<li> Collision Energy (float) </li>
<li> LibraryIntensity (float) </li>
<li> transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) </li>
<li> decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) </li>
<li> PeptideSequence (free text, sequence only (no modifications) ) </li>
<li> ProteinName (free text) </li>
<li> Annotation (free text, e.g. y7) </li>
<li> FullUniModPeptideName (free text, should contain modifications*) </li>
<li> PrecursorCharge (integer, contains the charge of the precursor) </li>
<li> GroupLabel (free text, e.g. heavy or light) </li>
<li> UniprotID (free text) </li>
<li> FragmentType (free text, contains the type of the fragment, e.g. "b" or "y") </li>
<li> FragmentCharge (integer, contains the fragment charge) </li>
<li> FragmentSeriesNumber (integer, e.g. for y7 use "7" here) </li>
</ul>
<p>
* modifications should be supplied inside the sequence using UniMod
identifiers or freetext identifiers that are understood by %OpenMS. Please do
not use the ambiguous bracket notation (e.g. PEPT[+80]IDE or PEPT[181]IDE)
since this is ambiguous and will NOT be interpreted correctly!
example: PEPT(Phosphorylation)IDE(UniMod:27)A )
</p>
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPConvertTSVToTraML : public TOPPBase
{
public:
TOPPConvertTSVToTraML() :
TOPPBase("ConvertTSVToTraML", "Converts an OpenSWATH transition TSV file to a TraML file")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input OpenSWATH transition TSV file.\n "
"See http://www.openms.de/current_doxygen/html/UTILS_ConvertTSVToTraML.html for format.");
/*
PrecursorMz (float) \n \
ProductMz (float)\n \
Tr_calibrated (float)\n \
transition_name (free text, needs to be unique) \n \
Collision Energy (float)\n \
LibraryIntensity (float) \n \
transition_group_id (free text, unique for each peptide) \n \
decoy (1 or 0 [no decoy]) \n \
PeptideSequence (free text, raw sequence) \n \
ProteinName (free text) \n \
Annotation (free text, e.g. y7) \n \
FullUniModPeptideName (free text, should contain modifications*) \n \
PrecursorCharge (integer, contains the charge of the precursor) \n \
GroupLabel (free text, e.g. heavy or light) \n \
UniprotID (free text) \n \
FragmentType (free text, contains the type of the fragment, e.g. 'b' or 'y') \n \
FragmentCharge (integer, contains the fragment charge) \n \
FragmentSeriesNumber (integer, e.g. for y7 use '7' here) \n \
*/
setValidFormats_("in", StringList::create("csv"));
registerOutputFile_("out", "<file>", "", "Output TraML file");
setValidFormats_("out", StringList::create("TraML"));
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
String out = getStringOption_("out");
const char * tr_file = in.c_str();
TraMLFile traml;
TargetedExperiment targeted_exp;
TransitionTSVReader tsv_reader = TransitionTSVReader();
std::cout << "Reading " << in << std::endl;
tsv_reader.setLogType(log_type_);
tsv_reader.convertTSVToTargetedExperiment(tr_file, targeted_exp);
tsv_reader.validateTargetedExperiment(targeted_exp);
std::cout << "Writing " << out << std::endl;
traml.store(out, targeted_exp);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPConvertTSVToTraML tool;
return tool.main(argc, argv);
}
/// @endcond
|
