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Commit f49c68dc authored by Olivier Langella's avatar Olivier Langella
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beta peptide output

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lib/libproteomicsvg.jar
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src/fr/inra/pappso/xtandempipeline/class_msms/GroupingProtein/PeptideMass.java
+ 9
− 1
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......@@ -46,7 +46,7 @@ public class PeptideMass implements Comparable<PeptideMass> {
private HashSampleScanSet hashSampleScanSet = new HashSampleScanSet();
/* List of hashSampleScans (scan number, charge) identifying this peptides */
private HashMap<MsRun, HashMap<Integer, Integer>> msRun2scanAndCharge = new HashMap<MsRun, HashMap<Integer, Integer>>();
private SubGroupSet subgroupSet;
private SubGroupSet subgroupSet = new SubGroupSet();
private Peptide bestEvaluePeptide = null;
......@@ -100,4 +100,12 @@ public class PeptideMass implements Comparable<PeptideMass> {
return sequenceLi + "-" + this.mh;
}
public SubGroupSet getSubGroupSet() {
return this.subgroupSet;
}
public HashSampleScanSet getHashSampleScanSet() {
return hashSampleScanSet;
}
}
src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
+ 62
− 40
View file @ f49c68dc
......@@ -41,9 +41,9 @@ import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMassSet;
import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashPeptideSet;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
public class OdsRedundantPeptideOutput {
private static final Logger logger = Logger
......@@ -87,31 +87,36 @@ public class OdsRedundantPeptideOutput {
}
/*
* langella@shyrka:~/developpement/git/groupingprotein/groupingprotein/build$ gp-read-xtandem.py /home/langella/protic-data/tests/xtandem/2008_07_17_AMIOUR_NARDJIS_325_1_0* | gp-grouping | gp-output-peptide-list.py
Finish reading parameter
Begin reading data
Read files : /home/langella/protic-data/tests/xtandem/2008_07_17_AMIOUR_NARDJIS_325_1_03_1348.xml
Read files : /home/langella/protic-data/tests/xtandem/2008_07_17_AMIOUR_NARDJIS_325_1_04_1610.xml
Finish loading data
Begin Peptide Reproductibility filter : 267
End Peptide Reproductibility filter : 267
Begin Minimun Peptide By Prot filter : 124
End Minimun Peptide By Prot filter : 84
Begin Grouping
End subgroup creation : 34
Search non informative subgroup
Index and Order group result
End group creation : 14
Begin Export
Group Peptide Sequence Modifs MhTheo Charges Subgroups Spectra
a1 pep.a1 GSGFGGGSGFGGGSGFSGGGFGGGGFGGGR 2399.019 2 a1.a2 2
a1 pep.a2 GSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYR 3312.309 3 a1.a1 2
a1 pep.a3 HGGGGGGFGGGGFGSR 1320.583 2|3 a1.a2 3
a1 pep.a4 TSQNSELNNMQDLVEDYK 2127.95 2 a1.a2 2
a1 pep.a5 GSSSGGGYSSGSSSYGSGGR 1740.706 2 a1.a2 2
a1 pep.a6 GGGGGGYGSGGSSYGSGGGSYGSGGGGGGGR 2383.952 2|3 a1.a1 3
a1 pep.a7 GGSSSGGGYGSGGGGSSSVK 1588.684 2 a1.a2 2
a
* langella@shyrka:~/developpement/git/groupingprotein/groupingprotein/build$
* gp-read-xtandem.py
* /home/langella/protic-data/tests/xtandem/2008_07_17_AMIOUR_NARDJIS_325_1_0
* * | gp-grouping | gp-output-peptide-list.py Finish reading parameter
* Begin reading data Read files : /home/langella/protic-data/tests/xtandem/
* 2008_07_17_AMIOUR_NARDJIS_325_1_03_1348.xml Read files :
* /home/langella/protic
* -data/tests/xtandem/2008_07_17_AMIOUR_NARDJIS_325_1_04_1610.xml Finish
* loading data Begin Peptide Reproductibility filter : 267 End Peptide
* Reproductibility filter : 267 Begin Minimun Peptide By Prot filter : 124
* End Minimun Peptide By Prot filter : 84 Begin Grouping End subgroup
* creation : 34 Search non informative subgroup Index and Order group
* result End group creation : 14 Begin Export
*
*
* Group Peptide Sequence Modifs MhTheo Charges Subgroups Spectra
*
* a1 pep.a1 GSGFGGGSGFGGGSGFSGGGFGGGGFGGGR 2399.019 2 a1.a2 2
*
* a1 pep.a2 GSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYR 3312.309 3 a1.a1 2
*
* a1 pep.a3 HGGGGGGFGGGGFGSR 1320.583 2|3 a1.a2 3
*
* a1 pep.a4 TSQNSELNNMQDLVEDYK 2127.95 2 a1.a2 2
*
* a1 pep.a5 GSSSGGGYSSGSSSYGSGGR 1740.706 2 a1.a2 2
*
* a1 pep.a6 GGGGGGYGSGGSSYGSGGGSYGSGGGGGGGR 2383.952 2|3 a1.a1 3
*
* a1 pep.a7 GGSSSGGGYGSGGGGSSSVK 1588.684 2 a1.a2 2 a
*/
public void write(Identification ident) throws MSMSException {
try {
......@@ -122,19 +127,20 @@ a
for (HashSampleScanSetProt hashProt : sg
.getHashSampleScanSetProtList()) {
Protein prot = (Protein) hashProt.getGrpProtMatch()
.getGrpProtein();
for (Peptide peptide : ((Match) hashProt
.getGrpProtMatch())
.get_peptide_order_inclus_redon()) {
// first pass to index each ScanSample and give it a
// PeptideMass
PeptideMass pepMass = pepMassSet
.addPeptide(peptide);
pepMass.addSubGroup(sg);
// HashPeptide p = peptide.getHashPeptide();
//if (uniquePeptideSet.add(peptide.getHashPeptide())) {
// this.writeOnePeptide(group, sg, prot, peptide);
//}
// if
// (uniquePeptideSet.add(peptide.getHashPeptide()))
// {
// this.writeOnePeptide(group, sg, prot, peptide);
// }
}
}
......@@ -157,7 +163,9 @@ a
pepMass.addSubGroup(sg);
// HashPeptide p = peptide.getHashPeptide();
if (uniquePepMass.add(pepMass)) {
this.writeOnePeptide(group, sg, prot, peptide, pepMass);
// for each prot, give all PeptideMass
this.writeOnePeptide(group, sg, prot, peptide,
pepMass);
}
}
......@@ -193,10 +201,12 @@ a
odsTable.writeCell("Stop");
// odsTable.writeCell("E-value");
// odsTable.writeCell("Charge");
odsTable.writeCell("Charge");
// odsTable.writeCell("MH+ Obs");
// odsTable.writeCell("MH+ theo");
odsTable.writeCell("MH+ theo");
odsTable.writeCell("present in subgroups");
// odsTable.writeCell("DeltaMH+");
odsTable.writeCell("number of spectra");
// odsTable.writeCell("Delta-ppm");
} catch (XMLStreamException e) {
String message = "XMLStreamException in writeHeaders() "
......@@ -217,24 +227,36 @@ a
odsTable.writeCell(prot.get_description());
// odsTable.writeCell(peptide.get_sample());
odsTable.writeCell(pepMass.getHumanId());
//odsTable.writeCell(peptide.getSampleScan().getScan());
// odsTable.writeCell(peptide.getSampleScan().getScan());
// odsTable.writeCell(peptide.get_RT_in_sec());
odsTable.writeCell(peptide.getSequence());
odsTable.writeCell(peptide.get_Modifs_formater());
odsTable.writeCell(peptide.get_start());
odsTable.writeCell(peptide.get_stop());
//pepMass
// pepMass
// odsTable.writeCell(peptide.get_evalue());
// S.append("\t" + pep.get_evalue());
// odsTable.writeCell(peptide.get_charge());
odsTable.writeCell(peptide.get_charge());
// S.append("\t" + pep.get_charge());
// odsTable.writeCell(peptide.get_mhplus_obser());
// S.append("\t" + pep.get_mhplus_obser());
// odsTable.writeCell(peptide.get_mhplus_theo());
odsTable.writeCell(peptide.get_mhplus_theo());
// S.append("\t" + pep.get_mhplus_theo());
// odsTable.writeCell(peptide.get_deltamass());
SubGroupSet sgList = pepMass.getSubGroupSet();
String tagSg = "";
for (SubGroup sgOther : sgList) {
tagSg += group.getNumber() + "." + sgOther.getNumber() + " ";
}
tagSg = tagSg.trim();
odsTable.writeCell(tagSg);
// nbSpectra = pepMass.getNumberOfPsm();
odsTable.writeCell(pepMass.getHashSampleScanSet().size());
// S.append("\t" + pep.get_deltamass());
// odsTable.writeCell(((peptide.get_deltamass() / peptide
// .get_mhplus_theo()) * 1000000));
......
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