fix non sulfered molecular detection and remove mz < mzmincorestructure

brassinetGenouest/Readme.md

@@ -1,13 +1,38 @@
-### Genouest
+# Genouest jobs
 
+## Batch job
+
+check [slurm job](./slurm_genouest.sh)
+
+```shell
+sbatch --mem=20G slurm_genouest.sh
+```
+### Check job
+
+```shell
+squeue -u ofilangi
+```
+
+## Interactive job
+
+
+```shell
 srun --mem=20G --pty bash
 srun --mem=20G --cpus-per-task=8 --pty bash
+```
 
-sbatch --mem=20G script.sh
+### Set environment
 
+```shell
 . /local/env/envconda.sh
 export PATH=$HOME/bin:$PATH
 conda activate /home/genouest/inra_umr1349/ofilangi/sbt_env
+```
+
+### Example with blanc dataset
 
+```shell
+FILES="/groups/arch_igepp/metabolomics/MassSpectrometerOutputFile/brassimet/202111/Racines/MzXML*Neg/Brassinet_Racine_blanc-2_Neg_01_8540.mzXML"
+java -cp ../assembly/pack.jar fr.inrae.metabolomics.p2m2.MainDetection $FILES
+```
 
-squeue -u ofilangi

src/main/scala/fr/inrae/metabolomics/p2m2/MainDetection.scala

@@ -24,7 +24,7 @@ object MainDetection extends App {
                      endRT: Option[Double] = None,
                      overrepresentedPeak: Int = 800,
                      precisionMzh: Int = 1000,
-                     toleranceMz: Double = 0.01,
+                     toleranceMz: Double = 0.005,
                      warmup: Double = 0.50, // (30 sec)
                      outfile: Option[String] = None,
                      verbose: Boolean = false,
@@ -206,7 +206,8 @@ object MainDetection extends App {
           nbCarbonMax = confJson.numberCarbonMax(family),
           nbSulfurMin = confJson.numberSulfurMin(family),
           nbSulfurMax = confJson.numberSulfurMax(family),
-          config.toleranceMz,
+          minMzCoreStructure = confJson.minMzCoreStructure(family),
+          precisionDeltaM0M2 = config.toleranceMz,
           deltaMOM2 = confJson.deltaMp0Mp2(family))
 
     /**

src/main/scala/fr/inrae/metabolomics/p2m2/builder/ScanLoader.scala

@@ -6,7 +6,6 @@ import umich.ms.datatypes.spectrum.ISpectrum
 import umich.ms.fileio.filetypes.mzxml._
 
 import java.io.File
-import scala.Double.NaN
 import scala.jdk.CollectionConverters._
 import scala.math.sqrt
 import scala.util.{Success, Try}
@@ -150,17 +149,18 @@ case object ScanLoader {
   }
 
   def selectEligibleIons(
-                                          source: MZXMLFile,
-                                          index: MZXMLIndex,
-                                          start : Option[Double] = None,
-                                          end : Option[Double] = None,
-                                          noiseIntensity : Double,
-                                          nbCarbonMin: Double,
-                                          nbCarbonMax: Double,
-                                          nbSulfurMin : Double,
-                                          nbSulfurMax : Double,
-                                          precision: Double = 0.01,
-                                          deltaMOM2 : Double
+                          source: MZXMLFile,
+                          index: MZXMLIndex,
+                          start : Option[Double] = None,
+                          end : Option[Double] = None,
+                          noiseIntensity : Double,
+                          nbCarbonMin: Double,
+                          nbCarbonMax: Double,
+                          nbSulfurMin : Double,
+                          nbSulfurMax : Double,
+                          minMzCoreStructure : Double,
+                          precisionDeltaM0M2: Double,
+                          deltaMOM2 : Double
                                         ): Seq[PeakIdentification] = {
     println("\n== Search for isotopes sulfur == ")
     // the file using those numbers. We need the raw scan numbers (the numbers
@@ -178,8 +178,8 @@ case object ScanLoader {
         // remove the first one to compute Delta M
         mzValues
           .zipWithIndex
-          .filter { case (_, idx) =>
-            spectrum.getIntensities()(idx) > noiseIntensity
+          .filter { case (mz0, idx) =>
+            (spectrum.getIntensities()(idx) > noiseIntensity) && (mz0>minMzCoreStructure)
           }
           .map { case (mz0, idx0) =>
             val mz_ms_p2 = mz0 + deltaMOM2
@@ -190,7 +190,7 @@ case object ScanLoader {
             (mz0, idx0, mz1, idx1, mz_p2, idx2)
           }
           .filter { case (mz, _, _, _, mz2, _) =>
-            ((mz - mz2).abs - deltaMOM2).abs < precision
+            ((mz - mz2).abs - deltaMOM2).abs < precisionDeltaM0M2
           }
           /* criteria M1 of Isotope C are present at 1.1 and S are present 4.4 % */
           .filter { case (_, idx0, _, idx1, _, _) =>

src/main/scala/fr/inrae/metabolomics/p2m2/export/CsvIonsIdentificationFile.scala

@@ -30,7 +30,6 @@ case object CsvIonsIdentificationFile {
       bw.write(s"CHEBI;")
       //bw.write(s"BRACHEMDB;")
       bw.write(s"BRASSICA;")
-      bw.write("mz threshold;")
       bw.write("Nb (NL+DI);")
       bw.write(s"NL;")
       bw.write(s"DI;")
@@ -72,11 +71,6 @@ case object CsvIonsIdentificationFile {
               }) + "[R="+ ChemicalUtils.correlation(m.formula,metabolitesIdentificationId.ion.peaks.map( p=> p.abundance)) + "]"
           }
           bw.write(namesAndR.mkString(",")+";")
-          if ( metabolitesIdentificationId.ion.peaks.head.mz < configJson.minMzCoreStructure(familyMetabolite) ) {
-            bw.write("*;")
-          } else
-            bw.write(";")
-
           bw.write(s"${metabolitesIdentificationId.scoreIdentification};")
 
           neutralLosses

src/test/scala/fr/inrae/metabolomics/p2m2/builder/ScanLoaderTest.scala

@@ -3,7 +3,6 @@ package fr.inrae.metabolomics.p2m2.builder
 import utest.{TestSuite, Tests, test}
 
 import java.io.File
-import scala.Double.NaN
 
 object ScanLoaderTest extends TestSuite {
   val tests = Tests {
@@ -28,6 +27,8 @@ object ScanLoaderTest extends TestSuite {
           nbCarbonMax=0.0,
           2.0,
           5.0,
+          minMzCoreStructure = 0.01,
+          precisionDeltaM0M2 = 0.001,
           deltaMOM2 = 1.996
         )
       assert(v2.isEmpty)
@@ -46,6 +47,8 @@ object ScanLoaderTest extends TestSuite {
           nbCarbonMax = 25.0,
           2.0,
           0.0,
+          minMzCoreStructure = 0.01,
+          precisionDeltaM0M2 = 0.001,
           deltaMOM2 = 1.996
         )
       assert(v2.isEmpty)
@@ -64,6 +67,8 @@ object ScanLoaderTest extends TestSuite {
           nbCarbonMax = 25.0,
           2.0,
           1.0,
+          minMzCoreStructure = 0.01,
+          precisionDeltaM0M2 = 0.001,
           deltaMOM2 = 1.996
         )
       assert(v2.isEmpty)
@@ -83,6 +88,8 @@ object ScanLoaderTest extends TestSuite {
           nbCarbonMax = 25.0,
           2.0,
           5.0,
+          minMzCoreStructure = 0.01,
+          precisionDeltaM0M2 = 0.001,
           deltaMOM2 = 1.996
         )
       assert(v2.nonEmpty)

src/test/scala/fr/inrae/metabolomics/p2m2/diagnostic/DaughterIonsDiagTest.scala

@@ -9,7 +9,7 @@ object DaughterIonsDiagTest extends TestSuite {
   val tests : Tests = Tests {
     val v = ScanLoader.read(new File(getClass.getResource("/20181018-037.mzXML").getPath))
     val v2 = {
-      (ScanLoader.selectEligibleIons(
+      ScanLoader.selectEligibleIons(
         v._1,
         v._2,
         Some(11.5), // RT start
@@ -19,8 +19,10 @@ object DaughterIonsDiagTest extends TestSuite {
         nbCarbonMax = 20.0,
         nbSulfurMin = 2.0,
         nbSulfurMax = 5.0,
+        minMzCoreStructure = 0.01,
+        precisionDeltaM0M2 = 0.001,
         deltaMOM2 = 1.996
-      ))
+      )
     }
 
     test("test") {
@@ -35,8 +37,8 @@ object DaughterIonsDiagTest extends TestSuite {
       ).foldLeft(Map[Int,Int]())(
         (acc : Map[Int,Int],v : Seq[Int]) => {
           v.map( p2 => acc.get(p2) match {
-              case Some(s) => (p2 -> (s + 1))
-              case None => (p2 -> 1)
+              case Some(s) => p2 -> (s + 1)
+              case None => p2 -> 1
           }).toMap
         }
       ).toSeq.sortBy(_._2)

src/test/scala/fr/inrae/metabolomics/p2m2/export/CsvIonsIdentificationFileTest.scala

@@ -21,6 +21,8 @@ object CsvIonsIdentificationFileTest extends TestSuite {
       nbCarbonMax = 20.0,
       nbSulfurMin = 2.0,
       nbSulfurMax = 5.0,
+      minMzCoreStructure = 0.01,
+      precisionDeltaM0M2 = 0.001,
       deltaMOM2 = 1.996
     )
 

src/test/scala/fr/inrae/metabolomics/p2m2/output/IonsIdentificationTest.scala

@@ -28,6 +28,8 @@ object IonsIdentificationTest extends TestSuite {
             nbCarbonMax = 20,
             nbSulfurMin = 2,
             nbSulfurMax = 5,
+            minMzCoreStructure = 0.01,
+            precisionDeltaM0M2 = 0.001,
             deltaMOM2 = 1.996,
             )) {
           assert(Try(read[PeakIdentification](write(elem))).isSuccess)