/**
* \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 <cmath>
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
#include "../../core/peptidextp.h"
#include "../../core/proteinmatch.h"
#include "../../core/peptideevidence.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,a-z,0-9,_]+)=(.*)$");
_regexp_parse_scan.setPattern(".*scan=([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() == "parameters")
{
while(!mime_parser.getCurrentTextStream().atEnd())
{
parseParametersLine(
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() == "masses")
{
while(!mime_parser.getCurrentTextStream().atEnd())
{
parseMassesLine(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());
}
saveAndClearPeptide();
}
else if(mime_parser.getCurrentFileName() == "decoy_summary")
{
_is_decoy_section = true;
while(!mime_parser.getCurrentTextStream().atEnd())
{
parseSummaryLine(mime_parser.getCurrentTextStream().readLine());
}
_is_decoy_section = false;
}
else if(mime_parser.getCurrentFileName() == "decoy_peptides")
{
_is_decoy_section = true;
while(!mime_parser.getCurrentTextStream().atEnd())
{
parsePeptidesLine(mime_parser.getCurrentTextStream().readLine());
}
saveAndClearPeptide();
_is_decoy_section = false;
}
else if(mime_parser.getCurrentFileName().startsWith("query"))
{
_current_query.query_index =
mime_parser.getCurrentFileName().mid(5).toULong();
while(!mime_parser.getCurrentTextStream().atEnd())
{
parseQueryLine(mime_parser.getCurrentTextStream().readLine());
}
saveQuery();
}
}
mime_parser.close();
qDebug() << "MascotDatParser::parse end";
}
void
MascotDatParser::parseMassesLine(const QString &masses_line)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< masses_line;
if(_regexp_header_line.exactMatch(masses_line))
{
QStringList header_list = _regexp_header_line.capturedTexts();
// C_term=17.002740
// N_term=1.007825
// delta1=15.994915,Oxidation (M)
if(header_list[1].startsWith("delta"))
{
_delta_modification_list.push_back(MascotModification());
unsigned index = header_list[1].mid(5).toUInt();
QStringList delta_mod_list = header_list[2].split(",");
pappso::pappso_double mass = delta_mod_list[0].toDouble();
if(delta_mod_list[1] == "Oxidation (M)")
{
_delta_modification_list[index - 1].modification =
pappso::AaModification::getInstance("MOD:00719");
_delta_modification_list[index - 1].residue = 'M';
}
else
{
_delta_modification_list[index - 1].modification =
pappso::AaModification::getInstanceCustomizedMod(mass);
}
//_number_of_residues = header_list[5].toUInt();
}
// FixedModResidues1=C
else if(header_list[1].startsWith("FixedModResidues"))
{
unsigned index = header_list[1].mid(16).toUInt();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< index;
_fixed_modification_list[index - 1].residue = header_list[2].at(0);
}
// NeutralLoss1=0.000000
// NeutralLoss1_master=63.998285
// FixedMod1=57.021464,Carbamidomethyl (C)
else if(header_list[1].startsWith("FixedMod"))
{
unsigned index = header_list[1].mid(8).toUInt();
_fixed_modification_list.push_back(MascotModification());
QStringList fixed_mod_list = header_list[2].split(",");
pappso::pappso_double mass = fixed_mod_list[0].toDouble();
//_number_of_residues = header_list[2].toUInt();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< header_list[2];
if(fixed_mod_list[1] == "Carbamidomethyl (C)")
{
_fixed_modification_list[index - 1].modification =
pappso::AaModification::getInstance("MOD:00397");
_fixed_modification_list[index - 1].residue = 'C';
}
else
{
_fixed_modification_list[index - 1].modification =
pappso::AaModification::getInstanceCustomizedMod(mass);
}
}
}
else
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " QREGEXP does not work on " << masses_line;
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _fixed_modification_list.size();
}
void
MascotDatParser::parseProteinLine(const QString &protein_line)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< protein_line;
ProteinXtpSp sp_xtp_protein;
// 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();
FastaFileSp fasta_file_sp =
_fasta_file_list[protein_list[1].toUInt() - 1];
_current_protein.setAccession(protein_list[2]);
_current_protein.setDescription(protein_list[4]);
_current_protein.setFastaFileP(fasta_file_sp.get());
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();
FastaFileSp fasta_file_sp = _fasta_file_list[0];
_current_protein.setAccession(protein_list[1]);
_current_protein.setDescription(protein_list[3]);
_current_protein.setFastaFileP(fasta_file_sp.get());
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);
_summary_list.resize(_number_of_queries);
_decoy_query_peptide_results.resize(_number_of_queries);
_decoy_summary_list.resize(_number_of_queries);
}
// min_peaks_for_homology=6
// max_hits=50
// version=2.5.0
else if(header_list[1] == "version")
{
_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::parseParametersLine(const QString &header_line)
{
if(_regexp_header_line.exactMatch(header_line))
{
QStringList header_list = _regexp_header_line.capturedTexts();
/*
* LICENSE=licence du logiciel
MP=
NM=
COM=WP4 Batch4 inj2 paramSTR QEKAC160601_02.raw.mgf
IATOL=
IA2TOL=
IASTOL=
IBTOL=
IB2TOL=
IBSTOL=
IYTOL=
IY2TOL=
IYSTOL=
SEG=
SEGT=
SEGTU=
LTOL=
TOL=5
TOLU=ppm
ITH=
ITOL=70
ITOLU=mmu
PFA=1
DB=Contaminants_WP4_D
DB2=S_cerevisiae_D
DB3=UPS1UPS2_D
MODS=Carbamidomethyl (C)
MASS=Monoisotopic
CLE=Trypsin/P
FILE=F:\MSData\Batch4 Qex+TOUL Injection2\QEKAC160601_02.raw.mgf
PEAK=
QUE=
TWO=
SEARCH=MIS
USERNAME=AMH
USEREMAIL=
CHARGE=2+ and 3+
INTERMEDIATE=
REPORT= AUTO
OVERVIEW=
FORMAT=Mascot generic
FORMVER=1.01
FRAG=
IT_MODS=Acetyl (Protein N-term),Oxidation (M)
USER00=
USER01=
USER02=
USER03=
USER04=
USER05=
USER06=
USER07=
USER08=
USER09=
USER10=
USER11=
USER12=
PRECURSOR=
TAXONOMY=All entries
ACCESSION=
REPTYPE=
SUBCLUSTER=
ICAT=
INSTRUMENT=ESI FTMS HCD
ERRORTOLERANT=
FRAMES=
CUTOUT=
USERID=0
QUANTITATION=
DECOY=
PEP_ISOTOPE_ERROR=
MULTI_SITE_MODS=
DATAURL=
RULES=1,2,4,5,6,7,8,9,10,13,14,15,17,18
INTERNALS=0.0,700.0
*/
if(header_list[1] == "FILE")
{
// FILE=F:\MSData\Batch4 Qex+TOUL Injection2\QEKAC160601_02.raw.mgf
_p_identification_data_source->getMsRunSp().get()->setFilename(
header_list[2]);
QFileInfo fileinfo(header_list[2]);
if(fileinfo.fileName() == header_list[2])
{
fileinfo.setFile(header_list[2].replace("\\", "/"));
_p_identification_data_source->getMsRunSp().get()->setSampleName(
fileinfo.baseName());
}
else
{
_p_identification_data_source->getMsRunSp().get()->setSampleName(
fileinfo.baseName());
}
}
}
}
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("_");
QString query_index_str = index_list[0];
unsigned int query_index_number = query_index_str.mid(1).toUInt();
QString peptide_index = index_list[1];
std::size_t current_peptide_index = peptide_index.mid(1).toUInt();
if((value != "-1") &&
((query_index_number != _current_peptide.query_index) ||
(current_peptide_index != _current_peptide.peptide_index)))
{
saveAndClearPeptide();
}
_current_peptide.query_index = query_index_number;
_current_peptide.peptide_index = current_peptide_index;
if(index_list.size() == 4)
{
if((index_list[2] == "primary") && (index_list[3] == "nl"))
{
// throw pappso::PappsoException(
// QObject::tr("primary_nl is not taken into account"));
}
}
else 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));
value = value.mid(2);
}
}
// 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
{
// 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(",\"");
}
}
/*
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
*/
// q24878_p3_primary_nl=000000020000000
/*
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 near q%3_p%4")
.arg(peptide_line)
.arg(exception_pappso.qwhat())
.arg(_current_peptide.query_index)
.arg(_current_peptide.peptide_index);
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 near q%3_p%4")
.arg(peptide_line)
.arg(exception_std.what())
.arg(_current_peptide.query_index)
.arg(_current_peptide.peptide_index);
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
}
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
// title=controllerType%3d0%20controllerNumber%3d1%20scan%3d43355
if(index == "title")
{
_current_query.parsed_scan_number = 0;
_current_query.title =
QUrl::fromPercentEncoding(value.toLatin1());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " " << _current_query.title;
if(_regexp_parse_scan.exactMatch(_current_query.title))
{
_current_query.parsed_scan_number =
_regexp_parse_scan.capturedTexts()[1].toULong();
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " " << _current_query.parsed_scan_number;
}
// rtinseconds=5703.84
else if(index == "rtinseconds")
{
_current_query.rt = value.toDouble();
}
// index=44035
else if(index == "index") // it is not the query index
{
_current_query.index = value.toUInt();
if(_current_query.parsed_scan_number == 0)
{
_current_query.parsed_scan_number = _current_query.index;
}
}
// charge=2+
else if(index == "charge")
{
_current_query.charge = value.mid(0, value.size() - 1).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)
{
std::vector<SummaryLine> *p_summary_list = &_summary_list;
if(_is_decoy_section)
{
p_summary_list = &_decoy_summary_list;
}
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();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< query_index << " " << index;
//_current_query.title = value;
(*p_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;
(*p_summary_list)[query_index - 1].match = value.toDouble();
}
// qplughole1=14.820890
else if(index.startsWith("qplughole"))
{
unsigned int query_index = index.mid(9).toUInt();
//_current_query.title = value;
(*p_summary_list)[query_index - 1].plug_hole = value.toDouble();
}
}
}
void
MascotDatParser::saveAndClearPeptide()
{
// qDebug() << "MascotDatParser::saveAndClearPeptide begin";
if(_current_peptide.query_index > 0)
{
// save
if(_is_decoy_section)
{
_decoy_query_peptide_results[_current_peptide.query_index - 1]
.push_back(_current_peptide);
}
else
{
_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() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_current_query.query_index > 0)
{
try
{
std::vector<PeptideLine> peptide_list =
_query_peptide_results[_current_query.query_index - 1];
savePeptideList(peptide_list, false);
peptide_list =
_decoy_query_peptide_results[_current_query.query_index - 1];
savePeptideList(peptide_list, true);
}
catch(pappso::PappsoException &error)
{
throw pappso::PappsoException(
QObject::tr("ERROR saving MASCOT query%1 :\n %2")
.arg(_current_query.query_index)
.arg(error.qwhat()));
}
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
bool is_decoy)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _current_query.query_index;
try
{
PeptideEvidence peptide_evidence_generic(
_p_identification_data_source->getMsRunSp().get(),
_current_query.parsed_scan_number);
peptide_evidence_generic.setCharge(_current_query.charge);
peptide_evidence_generic.setChecked(true);
peptide_evidence_generic.setExperimentalMass(
_summary_list[_current_query.query_index - 1].exp_mass);
peptide_evidence_generic.setRetentionTime(_current_query.rt);
peptide_evidence_generic.setIdentificationDataSource(
_p_identification_data_source);
// parse and save
for(PeptideLine &peptide_line : peptide_list)
{
if(peptide_line.peptide_string_list.size() == 0)
{
// no results
continue;
}
PeptideEvidence peptide_evidence(peptide_evidence_generic);
/*
*
0 setMissedCleavages(Integer.parseInt(st.nextToken()));
1 setPeptideMr(Double.parseDouble(st.nextToken()));
2 setDeltaMass(Double.parseDouble(st.nextToken()));
3 setNumberOfIonsMatched(Integer.parseInt(st.nextToken()));
4 setSequence(st.nextToken());
5 setPeaksUsedFromIons1(Integer.parseInt(st.nextToken()));
6 setVariableModificationsArray(st.nextToken());
7 setIonsScore(Double.parseDouble(st.nextToken()));
8 parseIonSeries(st.nextToken());
9 setPeaksUsedFromIons2(Integer.parseInt(st.nextToken()));
10 setPeaksUsedFromIons3(Integer.parseInt(st.nextToken()));
*/
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(peptide_line.peptide_string_list.size() < 8)
{
throw pappso::PappsoException(
QObject::tr("unable to parse ion score in peptide line q%1_p%2")
.arg(peptide_line.query_index)
.arg(peptide_line.peptide_index));
}
pappso::pappso_double ion_score =
peptide_line.peptide_string_list.at(7).toDouble();
peptide_evidence.setParam(PeptideEvidenceParam::mascot_score,
QVariant(ion_score));
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(is_decoy)
{
peptide_evidence.setEvalue(getEvalue(
ion_score,
_decoy_summary_list.at(_current_query.query_index - 1),
0.05));
}
else
{
peptide_evidence.setEvalue(
getEvalue(ion_score,
_summary_list.at(_current_query.query_index - 1),
0.05));
}
peptide_evidence.setParam(
PeptideEvidenceParam::mascot_expectation_value,
QVariant(peptide_evidence.getEvalue()));
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
QString peptide_str = peptide_line.peptide_string_list.at(4);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
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();
// variable modifications :
setVariableModifications(peptide_sp,
peptide_line.peptide_string_list.at(6));
// fixed modifications :
for(unsigned int i = 0; i < peptide_str.size(); i++)
{
for(MascotModification mascot_modif : _fixed_modification_list)
{
if(peptide_str.at(i) == mascot_modif.residue)
{
peptide_sp.get()->addAaModification(
mascot_modif.modification, i);
}
}
}
peptide_evidence.setPeptideXtpSp(
_p_project->getPeptideStore().getInstance(peptide_sp));
// qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" <<
// peptide_str << " evalue=" << peptide_evidence.getEvalue() << "
// ionscore=" << ion_score;
unsigned int i = 0;
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);
if(is_decoy)
{
accession = QString("%1|reversed").arg(accession);
}
// 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() - 1;
unsigned int stop = position_list.at(2).toUInt() - 1;
// qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
ProteinXtp protein;
protein.setAccession(accession);
if(peptide_line.fasta_file_list.size() == 0)
{
if(_fasta_file_list.size() == 1)
{
protein.setFastaFileP(_fasta_file_list[0].get());
}
else
{
throw pappso::PappsoException(
QObject::tr("ERROR no FASTA file"));
}
}
else
{
if(i < peptide_line.fasta_file_list.size())
{
protein.setFastaFileP(
peptide_line.fasta_file_list[i].get());
}
else
{
throw pappso::PappsoException(
QObject::tr("ERROR no corresponding FASTA file %1")
.arg(i));
}
}
if(is_decoy)
{
protein.setIsDecoy(true);
}
ProteinMatch *p_protein_match =
_p_identification_group->getProteinMatchInstance(accession);
if(p_protein_match == nullptr)
{
throw pappso::PappsoException(
QObject::tr("ERROR (p_protein_match == nullptr) %1")
.arg(str));
}
// qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
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);
i++;
}
}
}
catch(pappso::PappsoException exception_pappso)
{
_error_str = QObject::tr(
"ERROR in MascotDatParser::savePeptideList "
" PAPPSO exception:\n%2")
.arg(exception_pappso.qwhat());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
catch(std::exception exception_std)
{
_error_str = QObject::tr(
"ERROR in MascotDatParser::savePeptideList std "
"exception:\n%2")
.arg(exception_std.what());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
pappso::pappso_double
MascotDatParser::getEvalue(pappso::pappso_double ion_score,
SummaryLine &summary_line,
pappso::pappso_double confidence_interval) const
{
pappso::pappso_double identity_threshold =
(pappso::pappso_double)10.0 *
std::log(summary_line.match /
(confidence_interval * (pappso::pappso_double)20.0)) /
log((pappso::pappso_double)10);
;
return (confidence_interval *
pow((pappso::pappso_double)10,
((identity_threshold - ion_score) / (pappso::pappso_double)10)));
}
pappso::pappso_double
MascotDatParser::getEvalueExperimental(
pappso::pappso_double ion_score,
SummaryLine &summary_line,
pappso::pappso_double confidence_interval) const
{
// Evalue experimental Homology threshold (QPlughole value from .dat file).
pappso::pappso_double eval =
(ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}
void
MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
QString variable_modifications_string)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< variable_modifications_string;
//
for(unsigned int i = 0; i < variable_modifications_string.size(); i++)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< variable_modifications_string.mid(i, 1).toUInt() << " "
<< variable_modifications_string;
if(variable_modifications_string.mid(i, 1).toUInt() > 0)
{
MascotModification mascot_modification = _delta_modification_list
[variable_modifications_string.mid(i, 1).toUInt() - 1];
try
{
if(i > 0)
{
peptide_sp.get()->addAaModification(
mascot_modification.modification, i - 1);
}
else
{
peptide_sp.get()->addAaModification(
mascot_modification.modification, i);
}
}
catch(pappso::PappsoException &error)
{
throw pappso::PappsoException(
QObject::tr("ERROR adding modification %1 to peptide %2 at "
"position %3 :\n %4")
.arg(mascot_modification.modification->getAccession())
.arg(peptide_sp.get()->toAbsoluteString())
.arg(i)
.arg(error.qwhat()));
}
}
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}