Newer
Older
/**
* \file /input/mascot/mascotdatparser.h
* \date 17/2/2018
* \author Olivier Langella
* \brief MASCOT dat file parser
*/
/*******************************************************************************
* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp 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.
*
* XTPcpp 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 XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
******************************************************************************/
#include "mascotdatparser.h"
#include "mimeparser.h"
#include "../../core/peptidextp.h"
#include "../../core/proteinmatch.h"
MascotDatParser::MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
IdentificationDataSource * p_identification_data_source) {
_p_project = p_project;
_p_identification_group = p_identification_group;
_p_identification_data_source = p_identification_data_source;
_regexp_header_line.setPattern("^([a-z,0-9,_]+)=(.*)$");
}
MascotDatParser::~MascotDatParser() {
}
void MascotDatParser::parse(QIODevice * in_stream) {
qDebug() << "MascotDatParser::parse begin";
MimeParser mime_parser(in_stream);
mime_parser.open();
for(bool more=mime_parser.goToFirstFile(); more; more=mime_parser.goToNextFile()) {
qDebug() << "MascotDatParser::parse mimetype=" << mime_parser.getCurrentMimeType() << " filename=" << mime_parser.getCurrentFileName();
if (mime_parser.getCurrentFileName() == "proteins") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseProteinLine( mime_parser.getCurrentTextStream().readLine());
}
}
else if (mime_parser.getCurrentFileName() == "header") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
}
}
else if (mime_parser.getCurrentFileName() == "summary") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseSummaryLine( mime_parser.getCurrentTextStream().readLine());
}
}
else if (mime_parser.getCurrentFileName() == "peptides") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parsePeptidesLine( mime_parser.getCurrentTextStream().readLine());
}
else if (mime_parser.getCurrentFileName().startsWith("query")) {
_current_query_index = mime_parser.getCurrentFileName().mid(5).toUInt();
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseQueryLine( mime_parser.getCurrentTextStream().readLine());
}
saveQuery();
}
}
mime_parser.close();
qDebug() << "MascotDatParser::parse end";
}
void MascotDatParser::parseProteinLine(const QString & protein_line) {
//02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
if (regexp_protein.exactMatch(protein_line)) {
QStringList protein_list = regexp_protein.capturedTexts();
_current_protein.setAccession(protein_list[2]);
_current_protein.setDescription(protein_list[4]);
sp_xtp_protein = _current_protein.makeProteinXtpSp();
sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
}
else {
QRegExp regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
if (regexp_proteinb.exactMatch(protein_line)) {
QStringList protein_list = regexp_proteinb.capturedTexts();
_current_protein.setAccession(protein_list[1]);
_current_protein.setDescription(protein_list[3]);
sp_xtp_protein = _current_protein.makeProteinXtpSp();
sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
}
else {
qDebug() << "MascotDatParser::parseProteinLine error " << protein_line;
}
}
}
void MascotDatParser::parseHeaderLine(const QString & header_line) {
if (_regexp_header_line.exactMatch(header_line)) {
QStringList header_list = _regexp_header_line.capturedTexts();
//sequences=73998
//sequences_after_tax=73998
//residues=24900901
if (header_list[1].startsWith("residues")) {
qDebug() << "queries=" << header_list[2];
_number_of_residues = header_list[2].toUInt();
}
//distribution=64847,0,1,576,2254,1934,1417,984,683,419,238,192,113,89,74,46,23,32,28,21,11,3,2,3,3,2,1,1,0,0,0,0,0,0,1
//decoy_type=1
//distribution_decoy=65162,0,1,552,2259,1891,1422,957,601,376,192,159,126,73,56,64,26,27,22,14,6,4,1,1,3,2,1
//exec_time=484
//date=1517587671
//time=17:07:51
//queries=54084
else if (header_list[1].startsWith("queries")) {
qDebug() << "queries=" << header_list[2];
_number_of_queries = header_list[2].toUInt();
_query_peptide_results.resize(_number_of_queries);
//min_peaks_for_homology=6
//max_hits=50
//version=2.5.0
_p_identification_data_source->setIdentificationEngineVersion(header_list[2]);
}
//fastafile=C:/inetpub/mascot/sequence/ECOLI_INRA/current/ECOLI_INRA_1.fasta
else if (header_list[1].startsWith("fastafile")) {
qDebug() << "fastafile=" << header_list[2];
_fasta_file_list.push_back( _p_project->getFastaFileStore().getInstance(FastaFile(header_list[2])));
_p_identification_data_source->addFastaFile(_fasta_file_list.back());
}
//release=ECOLI_INRA_1.fasta
//sequences1=4305
//sequences_after_tax1=4305
//residues1=1356026
//fastafile2=C:/inetpub/mascot/sequence/HUMAN_INRA/current/HUMAN_INRA_1.fasta
//release2=HUMAN_INRA_1.fasta
//sequences2=69693
//sequences_after_tax2=69693
//residues2=23544875
//taskid=151758718701
}
}
void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
try {
if (_regexp_header_line.exactMatch(peptide_line)) {
QStringList header_list = _regexp_header_line.capturedTexts();
QString index = header_list[1];
QString value = header_list[2];
QStringList index_list = index.split("_");
if (index_list.size() == 3) {
if (index_list[2] == "db") {
//q1_p1_db=02
while (value.size() > 0) {
QString fasta_str = value.mid(0,2);
_current_peptide.fasta_file_list.push_back(_fasta_file_list.at(fasta_str.toInt()-1));
//q856_p9_subst=1,X,W
else if (index_list[2] == "subst") {
_current_peptide.subst = value;
}
else if (index_list.size() == 2) {
if (value == "-1") {
//no result for this query
}
else {
QString query_index = index_list[0];
_current_peptide.query_index = query_index.mid(1).toUInt();
_current_peptide.peptide_index = peptide_index.mid(1).toUInt();
//q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
int position = value.indexOf(";\"", 0);
QString peptide_string = value.mid(0, position);
qDebug() << "peptide_string=" << peptide_string;
_current_peptide.peptide_string_list = peptide_string.split(",");
QString protein_string = value.mid(position+2);
qDebug() << "protein_string=" << protein_string;
//"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
_current_peptide.protein_string_list = protein_string.split(",\"");
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
}
}
/*
q1_p1_db=02
q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
q1_p1_terms=K,L
q1_p2_db=02
q1_p2=1,598.296219,0.003987,2,KEEPP,11,0000000,1.32,0002000000000000000,0,0;"tr|E9PNM8|E9PNM8_HUMAN":0:134:138:1
q1_p2_terms=R,-
q2_p1_db=02
q2_p1=1,598.380234,-0.000316,3,KAGVPK,13,00000000,17.13,0002011000000000000,0,0;"tr|H7C1P9|H7C1P9_HUMAN":0:945:950:2
q2_p1_terms=K,K
q2_p2_db=0202
q2_p2=1,598.380234,-0.000316,2,KQPVK,9,0000000,9.54,0002011000000000000,0,0;"sp|P33527|MRP1_HUMAN":0:270:274:1,"tr|I3L4X2|I3L4X2_HUMAN":0:169:173:1
q2_p2_terms=R,V:R,V
q2_p3_db=02
q2_p3=1,598.380234,-0.000316,2,KAVPGK,13,00000000,7.03,0002001000000000000,0,0;"sp|Q13061|TRDN_HUMAN":0:440:445:2
q2_p3_terms=K,K
q2_p4_db=0202
q2_p4=1,598.380234,-0.000316,2,IPGGKK,14,00000000,1.26,0002001000000000000,0,0;"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
q2_p4_terms=K,F:K,F
*/
/*
q856_p9_db=0202
q856_p9=0,685.427521,-0.000117,3,XLLVR,12,0000000,13.68,0000002000000000000,0,0;"tr|V9GY00|V9GY00_HUMAN":0:1:5:1,"tr|H7C3C3|H7C3C3_HUMAN":0:1:5:1
q856_p9_terms=-,L:-,V
q856_p9_subst=1,X,W
*/
}
catch (pappso::PappsoException exception_pappso) {
_error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, PAPPSO exception:\n%2").arg(peptide_line).arg(exception_pappso.qwhat());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
catch (std::exception exception_std) {
_error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, std exception:\n%2").arg(peptide_line).arg(exception_std.what());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
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
void MascotDatParser::parseQueryLine(const QString & query_line) {
try {
if (_regexp_header_line.exactMatch(query_line)) {
QStringList header_list = _regexp_header_line.capturedTexts();
QString index = header_list[1];
QString value = header_list[2];
//title=FULL%20ISSLGSVGAGIVAVKK%20N22213%20%20%20QEP1_SpikeIn_230914_1_3ng_270914%2e35282%2e35282%2e2
if (index == "title") {
_current_query.title = value;
}
//rtinseconds=5703.84
else if (index == "rtinseconds") {
_current_query.rt = value.toDouble();
}
//index=44035
else if (index == "index") {
_current_query.query_index = value.toUInt();
}
//charge=2+
else if (index == "charge") {
_current_query.charge = value.toUInt();
}
}
/*
mass_min=129.102051
mass_max=1198.751099
int_min=2327
int_max=6.845e+005
num_vals=44
num_used1=-1
Ions1=129.102051:1.111e+005,275.207306:9.008e+004,374.275299:9.717e+004,514.825623:1.929e+004,599.878906:1.472e+005,714.431519:1.356e+004,815.466003:9643,924.570435:4428,1028.645630:1.257e+005,1085.665527:6.845e+005,1198.751099:1.858e+005,147.112656:7.954e+004,261.159271:4.327e+004,357.248169:2.192e+004,506.312775:3319,543.336548:1.083e+005,655.376465:9786,1011.625977:1.747e+004,1068.641602:9.804e+004,1181.725342:2.712e+004,130.086014:3.602e+004,257.197388:1.455e+004,357.212097:3960,591.370056:2.454e+004,972.547058:3819,1069.647583:4.457e+004,201.123077:1.566e+004,299.171783:1.421e+004,534.825562:1.036e+004,1087.671631:2.374e+004,173.128418:1.512e+004,244.129089:1.052e+004,590.873291:8065,1067.656006:2.235e+004,228.133957:1.35e+004,258.180115:3194,534.333374:3635,1096.635376:1.549e+004,200.139084:1.026e+004,535.328552:3006,1070.637085:4813,183.112442:9925,131.080994:4806,211.108139:2327
*/
}
catch (pappso::PappsoException exception_pappso) {
_error_str = QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, PAPPSO exception:\n%2").arg(query_line).arg(exception_pappso.qwhat());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
catch (std::exception exception_std) {
_error_str = QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, std exception:\n%2").arg(query_line).arg(exception_std.what());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
}
void MascotDatParser::parseSummaryLine(const QString & summary_line) {
if (_regexp_header_line.exactMatch(summary_line)) {
QStringList header_list = _regexp_header_line.capturedTexts();
QString index = header_list[1];
QString value = header_list[2];
//qmass1=598.300206
if (index.startsWith("qmass")) {
unsigned int query_index = index.mid(5).toUInt();
//_current_query.title = value;
_summary_list[query_index-1].exp_mass=value.toDouble();
}
//qexp1=300.157379,2+
//qintensity1=2054822.6250
//qmatch1=73
else if (index.startsWith("qmatch")) {
unsigned int query_index = index.mid(6).toUInt();
//_current_query.title = value;
_summary_list[query_index-1].match=value.toDouble();
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
}
//qplughole1=14.820890
else if (index.startsWith("qplughole")) {
unsigned int query_index = index.mid(9).toUInt();
//_current_query.title = value;
_summary_list[query_index-1].plug_hole=value.toDouble();
}
}
}
void MascotDatParser::saveAndClearPeptide() {
qDebug() << "MascotDatParser::saveAndClearPeptide begin";
if (_current_peptide.query_index > 0) {
// save
_query_peptide_results[_current_peptide.query_index-1].push_back(_current_peptide);
}
//new peptide query clear
_current_peptide.peptide_string_list.clear();
_current_peptide.fasta_file_list.clear();
_current_peptide.query_index = 0;
_current_peptide.subst = "";
qDebug() << "MascotDatParser::saveAndClearPeptide end";
}
void MascotDatParser::saveQuery() {
qDebug() << "MascotDatParser::saveQuery begin";
if (_current_query.query_index > 0) {
std::vector< PeptideLine> peptide_list = _query_peptide_results[_current_query.query_index-1];
PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
peptide_evidence.setCharge(_current_query.charge);
peptide_evidence.setChecked(true);
peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
peptide_evidence.setRetentionTime(_current_query.rt);
peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
//parse and save
for(PeptideLine & peptide_line:peptide_list) {
pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
peptide_evidence.setEvalue(getEvalue(ion_score, _current_query.query_index, 0.05));
peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
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
428
429
430
431
432
433
434
435
QString peptide_str =peptide_line.peptide_string_list.at(4);
if (!peptide_line.subst.isEmpty()) {
//q856_p9_subst=1,X,W
//q24379_p2_subst=1,B,D,8,B,D
QStringList subst_list = peptide_line.subst.split(",");
for (unsigned int i=0; i < subst_list.size(); i+=3) {
peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
}
}
PeptideXtpSp peptide_sp;
peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
peptide_sp = _p_project->getPeptideStore().getInstance(peptide_sp);
if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
}
foreach (const QString &str, peptide_line.protein_string_list) {
//sp|O95006|OR2F2_HUMAN":0:299:303:1
int position = str.indexOf("\"", 0);
QString accession = str.mid(0, position);
qDebug() << "accession=" << accession;
QStringList position_list = str.mid(position+2).split(":");
if (position_list.size() != 4) {
throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
}
unsigned int start = position_list.at(1).toUInt();
unsigned int stop = position_list.at(2).toUInt();
ProteinXtp protein;
protein.setAccession(accession);
ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(protein.getAccession());
if (p_protein_match == nullptr) {
throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
}
ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
p_protein_match->setChecked(true);
PeptideMatch peptide_match;
peptide_match.setStart(start);
peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
p_protein_match->addPeptideMatch(peptide_match);
}
}
}
qDebug() << "MascotDatParser::saveQuery end";
}
pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval) const {
double identity_threshold = 10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * 20.0)) / log(10);;
return (confidence_interval * pow(10, ((identity_threshold - ion_score) / 10)));
}