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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2008 Spielberg Family Center for Applied Proteomics
// Cedars-Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/utility/misc/SHA1Calculator.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "pwiz/utility/misc/Std.hpp"
using namespace pwiz::cv;
using namespace pwiz::data;
using namespace pwiz::util;
using namespace pwiz::msdata;
namespace bfs = boost::filesystem;
void flush(SpectrumListSimple& sl, const string& nativeID, const string& msLevel,
const vector<MZIntensityPair>& pairs)
{
// fill in a new Spectrum and append it to the SpectrumList
SpectrumPtr spectrum(new Spectrum);
spectrum->index = sl.size();
spectrum->id = "scan=" + nativeID;
spectrum->set(MS_ms_level, msLevel);
spectrum->setMZIntensityPairs(pairs, MS_number_of_detector_counts);
sl.spectra.push_back(spectrum);
}
void txt2mzml(const char* filenameIn, const char* filenameOut)
{
// open input file
ifstream is(filenameIn);
if (!is)
throw runtime_error(("[txt2mzml] Unable to open file " + string(filenameIn)).c_str());
// allocate MSData object and SpectrumListSimple
MSData msd;
SpectrumListSimplePtr sl(new SpectrumListSimple);
msd.run.spectrumListPtr = sl;
// fill in some metadata
SourceFilePtr sourceFile(new SourceFile);
bfs::path p(filenameIn);
sourceFile->id = "text_data";
sourceFile->name = BFS_STRING(p.leaf());
sourceFile->location = string("file://") + BFS_COMPLETE(p.branch_path()).string();
string sha1 = SHA1Calculator::hashFile(filenameIn);
sourceFile->cvParams.push_back(CVParam(MS_SHA_1, sha1));
msd.fileDescription.sourceFilePtrs.push_back(sourceFile);
msd.run.id = "run";
// keep a simple state machine, flushing out cache to
// the MSData object when the nativeID changes
// cache
string nativeID;
string msLevel;
vector<MZIntensityPair> pairs;
while (is)
{
// parse stream one line at a time
string buffer;
getline(is, buffer);
// if we're done, flush one last time and break
if (!is)
{
flush(*sl, nativeID, msLevel, pairs);
break;
}
// tokenize the line
istringstream iss(buffer);
vector<string> tokens;
copy(istream_iterator<string>(iss), istream_iterator<string>(), back_inserter(tokens));
if (tokens.empty() || tokens[0]=="#") continue;
if (tokens.size() != 4 ||
tokens[1].size()<3 ||
tokens[1].substr(0,2)!="ms")
throw runtime_error((buffer + "\n[txt2mzml] Bad format.").c_str());
// flush cache when nativeID changes
if (tokens[0] != nativeID)
{
if (!nativeID.empty())
flush(*sl, nativeID, msLevel, pairs);
nativeID = tokens[0];
msLevel = tokens[1].substr(2);
pairs.clear();
}
// append m/z-intensity pair to cached binary data
pairs.push_back(MZIntensityPair(lexical_cast<double>(tokens[2]),
lexical_cast<double>(tokens[3])));
}
// write out mzML
MSDataFile::write(msd, filenameOut);
}
int main(int argc, char* argv[])
{
try
{
if (argc != 3)
{
cout << "Usage: txt2mzml fileIn fileOut\n"
<< "Read text spectrum data from fileIn, and write mzML to fileOut.\n"
<< "\n"
<< "Input format:\n"
<< "# scanNumber msLevel m/z intensity\n"
<< " 1 ms1 204.7596 1422.17\n"
<< " 1 ms1 204.7598 3215.49\n"
<< " [...]\n"
<< " 2 ms1 1999.7273 26.49\n"
<< " 2 ms1 1999.8182 0.00\n"
<< "\n"
<< "https://github.com/ProteoWizard\n"
<< "support@proteowizard.org\n";
return 1;
}
const char* filenameIn = argv[1];
const char* filenameOut = argv[2];
txt2mzml(filenameIn, filenameOut);
return 0;
}
catch (exception& e)
{
cerr << e.what() << endl;
}
catch (...)
{
cerr << "Caught unknown exception.\n";
}
return 1;
}
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