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 <QDebug>
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/peptide/peptide.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,_]+)=(.*)$");
}
MascotDatParser::~MascotDatParser() {
}
void MascotDatParser::parse(QIODevice * in_stream) {
qDebug() << "MascotDatParser::parse begin";
MimeParser mime_parser(in_stream);
mime_parser.open();
for(bool more=mime_parser.goToFirstFile(); more; more=mime_parser.goToNextFile()) {
qDebug() << "MascotDatParser::parse mimetype=" << mime_parser.getCurrentMimeType() << " filename=" << mime_parser.getCurrentFileName();
if (mime_parser.getCurrentFileName() == "proteins") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseProteinLine( mime_parser.getCurrentTextStream().readLine());
}
}
else if (mime_parser.getCurrentFileName() == "header") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
}
}
else if (mime_parser.getCurrentFileName() == "peptides") {
while(!mime_parser.getCurrentTextStream().atEnd()) {
parsePeptidesLine( mime_parser.getCurrentTextStream().readLine());
}
}
}
mime_parser.close();
qDebug() << "MascotDatParser::parse end";
}
void MascotDatParser::parseProteinLine(const QString & protein_line) {
//02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
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();
}
//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
_peptides_fasta_file_list.clear();
while (value.size() > 0) {
QString fasta_str = value.mid(0,2);
_peptides_fasta_file_list.push_back(_fasta_file_list.at(fasta_str.toInt()-1));
value = value.mid(2);
}
else if (index_list.size() == 2) {
if (value == "-1") {
//no result for this query
}
else {
QString query_index = index_list[0];
QString peptide_index = index_list[1];
//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;
QStringList peptide_string_list = peptide_string.split(",");
pappso::Peptide peptide(peptide_string_list.at(4));
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
QStringList protein_string_list = protein_string.split(",\"");
if (protein_string_list.size() != _peptides_fasta_file_list.size()) {
throw pappso::PappsoException(QObject::tr("ERROR (protein_string_list.size() != _peptides_fasta_file_list.size()) %1").arg(value));
}
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
225
226
227
228
229
230
231
232
233
234
235
236
237
foreach (const QString &str, 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(value));
}
unsigned int start = position_list.at(1).toUInt();
unsigned int stop = position_list.at(2).toUInt();
}
}
}
/*
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);