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Commit 58e8469d authored by Olivier Langella's avatar Olivier Langella
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parsing tandem version OK

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src/input/xtandemsaxhandler.cpp
+ 215
− 211
View file @ 58e8469d
...@@ -151,7 +151,7 @@ bool XtandemSaxHandler::startElement_note(QXmlAttributes attributes) { ...@@ -151,7 +151,7 @@ bool XtandemSaxHandler::startElement_note(QXmlAttributes attributes) {
_is_protein_description = true; _is_protein_description = true;
} }
} }
return is_ok; return is_ok;
} }
bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) { bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
...@@ -193,7 +193,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) { ...@@ -193,7 +193,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
bool is_ok = true; bool is_ok = true;
_current_text = _current_text.simplified().replace(" ", ""); _current_text = _current_text.simplified().replace(" ", "");
if (!_current_text.isEmpty()) { if (!_current_text.isEmpty()) {
//._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop() //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
_p_protein_match->getProteinXtpSp().get()->setSequence(_current_text.replace(QRegExp("\\*"), "")); _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text.replace(QRegExp("\\*"), ""));
} }
...@@ -204,76 +204,76 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) { ...@@ -204,76 +204,76 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
// pre="VLGR" post="VEFM" seq="TGSQGQCTQVR" missed_cleavages="10"> // pre="VLGR" post="VEFM" seq="TGSQGQCTQVR" missed_cleavages="10">
/* /*
* id * id
– the identifier for t – the identifier for t
his particular identified dom his particular identified dom
ain (s ain (s
pectrum pectrum
#).(i #).(i
d d
#).(dom #).(dom
ain#) ain#)
start start
– the first residue – the first residue
of t of t
he dom he dom
ain ain
end end
– the last residue – the last residue
of t of t
he dom he dom
ain ain
expect expect
– the expe – the expe
ctation va ctation va
lue for t lue for t
he peptide identification he peptide identification
mh mh
– the calculated pe – the calculated pe
ptide mass + a prot ptide mass + a prot
on on
delta delta
– the spectrum – the spectrum
mh m mh m
inus inus
the calculated m the calculated m
h h
hyperscore hyperscore
– T – T
ande ande
m’s score for t m’s score for t
he identification he identification
peak_count peak_count
– the num – the num
ber of pe ber of pe
aks that matched be aks that matched be
tween the theoretical tween the theoretical
and t and t
he test mass spectrum he test mass spectrum
pre pre
– the four re – the four re
sidue sidue
s pre s pre
ceding t ceding t
he dom he dom
ain ain
post post
– the four re – the four re
sidue sidue
s fol s fol
lowing t lowing t
he dom he dom
ain ain
seq seq
– the seque – the seque
nce of t nce of t
he dom he dom
ain ain
missed_cleavages missed_cleavages
– the num – the num
ber of pot ber of pot
ential cleavage sites in this ential cleavage sites in this
peptide seque peptide seque
nce*/ nce*/
// valeur généric du scan // valeur généric du scan
_current_peptide_sp = PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp(); _current_peptide_sp = PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp();
...@@ -332,151 +332,155 @@ bool XtandemSaxHandler::endElement_note() { ...@@ -332,151 +332,155 @@ bool XtandemSaxHandler::endElement_note() {
_p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1)); _p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1));
} }
else { else {
//<group label="input parameters" type="parameters"> //<group label="input parameters" type="parameters">
/* /*
* <note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note> * <note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note>
<note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/database.xml</note> <note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/database.xml</note>
<note type="input" label="output, histogram column width">30</note> <note type="input" label="output, histogram column width">30</note>
<note type="input" label="output, histograms">yes</note> <note type="input" label="output, histograms">yes</note>
<note type="input" label="output, maximum valid expectation value">0.05</note> <note type="input" label="output, maximum valid expectation value">0.05</note>
<note type="input" label="output, maximum valid protein expectation value">0.05</note> <note type="input" label="output, maximum valid protein expectation value">0.05</note>
<note type="input" label="output, one sequence copy">yes</note> <note type="input" label="output, one sequence copy">yes</note>
<note type="input" label="output, parameters">yes</note> <note type="input" label="output, parameters">yes</note>
<note type="input" label="output, path">/gorgone/pappso/formation/TD/xml_tandem/20120906_balliau_extract_1_A02_urzb-1.xml</note> <note type="input" label="output, path">/gorgone/pappso/formation/TD/xml_tandem/20120906_balliau_extract_1_A02_urzb-1.xml</note>
<note type="input" label="output, path hashing">no</note> <note type="input" label="output, path hashing">no</note>
<note type="input" label="output, performance">yes</note> <note type="input" label="output, performance">yes</note>
<note type="input" label="output, proteins">yes</note> <note type="input" label="output, proteins">yes</note>
<note type="input" label="output, results">valid</note> <note type="input" label="output, results">valid</note>
<note type="input" label="output, sequences">yes</note> <note type="input" label="output, sequences">yes</note>
<note type="input" label="output, sort results by">spectrum</note> <note type="input" label="output, sort results by">spectrum</note>
<note type="input" label="output, spectra">yes</note> <note type="input" label="output, spectra">yes</note>
<note type="input" label="output, xsl path">tandem-style.xsl</note> <note type="input" label="output, xsl path">tandem-style.xsl</note>
<note type="input" label="protein, C-terminal residue modification mass">0.0</note> <note type="input" label="protein, C-terminal residue modification mass">0.0</note>
<note type="input" label="protein, N-terminal residue modification mass">0.0</note> <note type="input" label="protein, N-terminal residue modification mass">0.0</note>
<note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note> <note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
<note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note> <note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
<note type="input" label="protein, cleavage semi">no</note> <note type="input" label="protein, cleavage semi">no</note>
<note type="input" label="protein, cleavage site">[RK]|{P}</note> <note type="input" label="protein, cleavage site">[RK]|{P}</note>
<note type="input" label="protein, modified residue mass file"></note> <note type="input" label="protein, modified residue mass file"></note>
<note type="input" label="protein, quick acetyl">yes</note> <note type="input" label="protein, quick acetyl">yes</note>
<note type="input" label="protein, quick pyrolidone">yes</note> <note type="input" label="protein, quick pyrolidone">yes</note>
<note type="input" label="protein, stP bias">yes</note> <note type="input" label="protein, stP bias">yes</note>
<note type="input" label="protein, taxon">usedefined</note> <note type="input" label="protein, taxon">usedefined</note>
<note type="input" label="refine">yes</note> <note type="input" label="refine">yes</note>
<note type="input" label="refine, cleavage semi">no</note> <note type="input" label="refine, cleavage semi">no</note>
<note type="input" label="refine, maximum valid expectation value">0.01</note> <note type="input" label="refine, maximum valid expectation value">0.01</note>
<note type="input" label="refine, modification mass">57.02146@C</note> <note type="input" label="refine, modification mass">57.02146@C</note>
<note type="input" label="refine, modification mass 1"></note> <note type="input" label="refine, modification mass 1"></note>
<note type="input" label="refine, point mutations">no</note> <note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, potential C-terminus modifications"></note> <note type="input" label="refine, potential C-terminus modifications"></note>
<note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note> <note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note>
<note type="input" label="refine, potential modification mass">15.99491@M</note> <note type="input" label="refine, potential modification mass">15.99491@M</note>
<note type="input" label="refine, potential modification mass 1"></note> <note type="input" label="refine, potential modification mass 1"></note>
<note type="input" label="refine, potential modification motif"></note> <note type="input" label="refine, potential modification motif"></note>
<note type="input" label="refine, potential modification motif 1"></note> <note type="input" label="refine, potential modification motif 1"></note>
<note type="input" label="refine, spectrum synthesis">yes</note> <note type="input" label="refine, spectrum synthesis">yes</note>
<note type="input" label="refine, unanticipated cleavage">no</note> <note type="input" label="refine, unanticipated cleavage">no</note>
<note type="input" label="refine, use potential modifications for full refinement">yes</note> <note type="input" label="refine, use potential modifications for full refinement">yes</note>
<note type="input" label="residue, modification mass">57.02146@C</note> <note type="input" label="residue, modification mass">57.02146@C</note>
<note type="input" label="residue, modification mass 1"></note> <note type="input" label="residue, modification mass 1"></note>
<note type="input" label="residue, potential modification mass">15.99491@M</note> <note type="input" label="residue, potential modification mass">15.99491@M</note>
<note type="input" label="residue, potential modification motif"></note> <note type="input" label="residue, potential modification motif"></note>
<note type="input" label="scoring, a ions">no</note> <note type="input" label="scoring, a ions">no</note>
<note type="input" label="scoring, b ions">yes</note> <note type="input" label="scoring, b ions">yes</note>
<note type="input" label="scoring, c ions">no</note> <note type="input" label="scoring, c ions">no</note>
<note type="input" label="scoring, cyclic permutation">yes</note> <note type="input" label="scoring, cyclic permutation">yes</note>
<note type="input" label="scoring, include reverse">yes</note> <note type="input" label="scoring, include reverse">yes</note>
<note type="input" label="scoring, maximum missed cleavage sites">1</note> <note type="input" label="scoring, maximum missed cleavage sites">1</note>
<note type="input" label="scoring, minimum ion count">4</note> <note type="input" label="scoring, minimum ion count">4</note>
<note type="input" label="scoring, x ions">no</note> <note type="input" label="scoring, x ions">no</note>
<note type="input" label="scoring, y ions">yes</note> <note type="input" label="scoring, y ions">yes</note>
<note type="input" label="scoring, z ions">no</note> <note type="input" label="scoring, z ions">no</note>
<note type="input" label="spectrum, dynamic range">100.0</note> <note type="input" label="spectrum, dynamic range">100.0</note>
<note type="input" label="spectrum, fragment mass type">monoisotopic</note> <note type="input" label="spectrum, fragment mass type">monoisotopic</note>
<note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note> <note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note>
<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note> <note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
<note type="input" label="spectrum, maximum parent charge">4</note> <note type="input" label="spectrum, maximum parent charge">4</note>
<note type="input" label="spectrum, minimum fragment mz">150.0</note> <note type="input" label="spectrum, minimum fragment mz">150.0</note>
<note type="input" label="spectrum, minimum parent m+h">500.0</note> <note type="input" label="spectrum, minimum parent m+h">500.0</note>
<note type="input" label="spectrum, minimum peaks">15</note> <note type="input" label="spectrum, minimum peaks">15</note>
<note type="input" label="spectrum, neutral loss mass">18.01057</note> <note type="input" label="spectrum, neutral loss mass">18.01057</note>
<note type="input" label="spectrum, neutral loss window">0.02</note> <note type="input" label="spectrum, neutral loss window">0.02</note>
<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note> <note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
<note type="input" label="spectrum, parent monoisotopic mass error plus">10</note> <note type="input" label="spectrum, parent monoisotopic mass error plus">10</note>
<note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note> <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note> <note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
*/ */
//<note type="input" label="spectrum, path">/gorgone/pappso/formation/TD/mzXML/20120906_balliau_extract_1_A02_urzb-1.mzXML</note> //<note type="input" label="spectrum, path">/gorgone/pappso/formation/TD/mzXML/20120906_balliau_extract_1_A02_urzb-1.mzXML</note>
if (_current_note_label == "spectrum, path") { if (_current_note_label == "spectrum, path") {
_sp_msrun.get()->setFilename(_current_text); _sp_msrun.get()->setFilename(_current_text);
} }
/* /*
<note type="input" label="spectrum, sequence batch size">1000</note> <note type="input" label="spectrum, sequence batch size">1000</note>
<note type="input" label="spectrum, threads">1</note> <note type="input" label="spectrum, threads">1</note>
<note type="input" label="spectrum, total peaks">100</note> <note type="input" label="spectrum, total peaks">100</note>
<note type="input" label="spectrum, use contrast angle">no</note> <note type="input" label="spectrum, use contrast angle">no</note>
<note type="input" label="spectrum, use neutral loss window">yes</note> <note type="input" label="spectrum, use neutral loss window">yes</note>
<note type="input" label="spectrum, use noise suppression">yes</note> <note type="input" label="spectrum, use noise suppression">yes</note>
</group> </group>
*/ */
//<group label="unused input parameters" type="parameters"> //<group label="unused input parameters" type="parameters">
/* /*
<note type="input" label="protein, use minimal annotations">yes</note> <note type="input" label="protein, use minimal annotations">yes</note>
<note type="input" label="refine, modification mass 2"></note> <note type="input" label="refine, modification mass 2"></note>
<note type="input" label="refine, potential modification mass 2"></note> <note type="input" label="refine, potential modification mass 2"></note>
<note type="input" label="refine, potential modification motif 2"></note> <note type="input" label="refine, potential modification motif 2"></note>
<note type="input" label="residue, modification mass 2"></note> <note type="input" label="residue, modification mass 2"></note>
<note type="input" label="residue, potential modification mass 1"></note> <note type="input" label="residue, potential modification mass 1"></note>
<note type="input" label="residue, potential modification mass 2"></note> <note type="input" label="residue, potential modification mass 2"></note>
<note type="input" label="residue, potential modification motif 1"></note> <note type="input" label="residue, potential modification motif 1"></note>
<note type="input" label="residue, potential modification motif 2"></note> <note type="input" label="residue, potential modification motif 2"></note>
<note type="input" label="scoring, pluggable scoring">no</note> <note type="input" label="scoring, pluggable scoring">no</note>
</group> </group>
*/ */
//<group label="performance parameters" type="parameters"> //<group label="performance parameters" type="parameters">
/* /*
<note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note> <note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note>
<note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note> <note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note>
<note label="list path, sequence source description #1">no description</note> <note label="list path, sequence source description #1">no description</note>
<note label="list path, sequence source description #2">no description</note> <note label="list path, sequence source description #2">no description</note>
<note label="modelling, duplicate peptide ids">6019</note> <note label="modelling, duplicate peptide ids">6019</note>
<note label="modelling, duplicate proteins">19735</note> <note label="modelling, duplicate proteins">19735</note>
<note label="modelling, estimated false positives">18</note> <note label="modelling, estimated false positives">18</note>
<note label="modelling, reversed sequence false positives">20</note> <note label="modelling, reversed sequence false positives">20</note>
<note label="modelling, spectrum noise suppression ratio">0.00</note> <note label="modelling, spectrum noise suppression ratio">0.00</note>
<note label="modelling, total peptides used">96618641</note> <note label="modelling, total peptides used">96618641</note>
<note label="modelling, total proteins used">273656</note> <note label="modelling, total proteins used">273656</note>
<note label="modelling, total spectra assigned">7464</note> <note label="modelling, total spectra assigned">7464</note>
<note label="modelling, total spectra used">12199</note> <note label="modelling, total spectra used">12199</note>
<note label="modelling, total unique assigned">6260</note> <note label="modelling, total unique assigned">6260</note>
<note label="process, start time">2013:12:20:16:47:19</note> <note label="process, start time">2013:12:20:16:47:19</note>
*/ */
//<note label="process, version">X! Tandem Sledgehammer (2013.09.01.1)</note> //<note label="process, version">X! Tandem Sledgehammer (2013.09.01.1)</note>
if (_current_note_label == "process, version") { if (_current_note_label == "process, version") {
_p_identification_data_source->setIdentificationEngineVersion(_current_text); QRegExp rx("\\((.*)\\)");
} if (rx.indexIn(_current_text, 0) != -1) {
/* _p_identification_data_source->setIdentificationEngineVersion(rx.cap(1));
<note label="quality values">243 476 437 382 384 417 399 416 346 387 390 382 321 355 311 283 253 272 251 228</note> }
<note label="refining, # input models">4893</note> qDebug() << "XtandemSaxHandler::endElement_note() " << _p_identification_data_source->getIdentificationEngineVersion();
<note label="refining, # input spectra">5520</note> }
<note label="refining, # partial cleavage">326</note> /*
<note label="refining, # point mutations">0</note> <note label="quality values">243 476 437 382 384 417 399 416 346 387 390 382 321 355 311 283 253 272 251 228</note>
<note label="refining, # potential C-terminii">0</note> <note label="refining, # input models">4893</note>
<note label="refining, # potential N-terminii">392</note> <note label="refining, # input spectra">5520</note>
<note label="refining, # unanticipated cleavage">0</note> <note label="refining, # partial cleavage">326</note>
<note label="timing, initial modelling total (sec)">170.96</note> <note label="refining, # point mutations">0</note>
<note label="timing, initial modelling/spectrum (sec)">0.0140</note> <note label="refining, # potential C-terminii">0</note>
<note label="timing, load sequence models (sec)">0.33</note> <note label="refining, # potential N-terminii">392</note>
<note label="timing, refinement/spectrum (sec)">0.0141</note> <note label="refining, # unanticipated cleavage">0</note>
</group> <note label="timing, initial modelling total (sec)">170.96</note>
*/ <note label="timing, initial modelling/spectrum (sec)">0.0140</note>
<note label="timing, load sequence models (sec)">0.33</note>
<note label="timing, refinement/spectrum (sec)">0.0141</note>
</group>
*/
} }
_current_text = ""; _current_text = "";
......
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