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
|
// --------------------------------------------------------------------------
// 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: Mathias Walzer $
// $Author: Mathias Walzer $
// --------------------------------------------------------------------------
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/QcMLFile.h>
#include <QByteArray>
#include <QFile>
#include <QString>
#include <QFileInfo>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
//~ #include <QIODevice>
#include <algorithm>
#include <fstream>
#include <vector>
#include <map>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_QCMerger QCMerger
@brief Merges two qcml files together.
<CENTER>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=3> \f$ \longrightarrow \f$ QCCalculator \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=2> @ref UTILS_QCCalculator </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref UTILS_QCShrinker </td>
</tr>
</table>
</CENTER>
The two or more given files (see parameter @p in) are merged. If a run/set exisits in several files, the qp of these are merged as well.
Several runs from qcml files can be comprised in a set.
- @p setname If the runs of the given input files are to be comprised in a set, this will be the name of the set.
Output is in qcML format (see parameter @p out) which can be viewed directly in a modern browser (chromium, firefox).
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_QCMerger.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_QCMerger.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPQCMerger :
public TOPPBase
{
public:
TOPPQCMerger() :
TOPPBase("QCMerger", "Merges two qcml files together.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFileList_("in", "<files>", StringList(), "List of qcml files to be merged.");
setValidFormats_("in", StringList::create("qcML"));
registerOutputFile_("out", "<file>", "", "Output extended/reduced qcML file");
setValidFormats_("out",StringList::create("qcML"));
registerStringOption_("setname", "<string>", "", "Use only when all given qcml files belong to one set, which will be held under the given name.", false);
}
void addBoxPlotQPs(std::map<String,String> nums, std::map<String,String> nams, String set, QcMLFile& qcmlfile)
{
for (std::map<String, String >::const_iterator it = nums.begin(); it != nums.end(); ++it)
{
QcMLFile::QualityParameter qp;
qp.name = nams[it->first]; ///< Name
qp.id = set + it->first; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = it->first;
qp.value = it->second;
qcmlfile.addSetQualityParameter(set, qp);
}
}
ExitCodes main_(int, const char **)
{
String plot_file = "";
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
StringList in_files = getStringList_("in");
String out = getStringOption_("out");
String setname = getStringOption_("setname");
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
QcMLFile qcmlfile;
for (Size i = 0; i < in_files.size(); ++i)
{
QcMLFile tmpfile;
tmpfile.load(in_files[i]);
qcmlfile.merge(tmpfile,setname);
}
// make #ms2 set stats
std::vector<String> ms2nums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000015", ms2nums_strings);
std::vector<Int> ms2nums;
for (std::vector<String>::iterator it = ms2nums_strings.begin(); it != ms2nums_strings.end(); ++it) //transform is too ugly and errorprone
{
ms2nums.push_back(it->toInt());
}
std::sort(ms2nums.begin(), ms2nums.end());
if (ms2nums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000043"] = String(ms2nums.front());
nams["QC:0000043"] = "min ms2 number";
nums["QC:0000044"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),25));
nams["QC:0000044"] = "Q1 ms2 number";
nums["QC:0000045"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),50));
nams["QC:0000045"] = "Q2 ms2 number";
nums["QC:0000046"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),75));
nams["QC:0000046"] = "Q3 ms2 number";
nums["QC:0000047"] = String(ms2nums.back());
nams["QC:0000047"] = "max ms2 number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
// make #id set stats
std::vector<String> idnums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000020", idnums_strings);
std::vector<Int> idnums;
for (std::vector<String>::iterator it = idnums_strings.begin(); it != idnums_strings.end(); ++it) //transform is too ugly and errorprone
{
idnums.push_back(it->toInt());
}
std::sort(idnums.begin(), idnums.end());
if (idnums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000053"] = String(idnums.front());
nams["QC:0000053"] = "min id numbers";
nums["QC:0000054"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),25));
nams["QC:0000054"] = "Q1 id numbers";
nums["QC:0000055"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),50));
nams["QC:0000055"] = "Q2 id numbers";
nums["QC:0000056"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),75));
nams["QC:0000056"] = "Q3 id numbers";
nums["QC:0000057"] = String(idnums.back());
nams["QC:0000057"] = "max id number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
qcmlfile.store(out);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPQCMerger tool;
return tool.main(argc, argv);
}
/// @endcond
|
