stream-reader-mzxml

A Scala library specializing in stream processing of mzXML files, based on FS2.

mzXML specifications

https://sashimi.sourceforge.net/schema_revision/mzXML_2.1/Doc/mzXML_2.0_tutorial.pdf

Installation using Docker

1) First option : build docker image

docker build . -t p2m2/stream-reader-mzxml

2) Second option : pull image from dockerhub

docker pull inraep2m2/stream-reader-mzxml

run command in the current directory

docker run -v $(pwd):/data inraep2m2/stream-reader-mzxml <MainClass> /data/myfile.mzXML

run command in specific path

docker run -v <path-where-is-mzXMLfile>:/data inraep2m2/stream-reader-mzxml <MainClass> /data/myfile.mzXML

Installation using sbt

sbt assembly

run command

java -cp ./assembly/pack.jar <MainClass> 

MainClass	Arguments	Description
MainDistributionIntensityIons		Number of ions by intensity thresholds
MainDistributionMzIons	Minimum intensity	Occurrences of the most frequent Mz (Ions)
MainDistributionDiffMzIons	Minimum intensity of peaks of interest	Gives the occurrences of the difference between the Mz (mass on charge) of interest and the other ions in the same mass spectrum to detect the formation of adducts.
MainPrecursorMzMatchingGlucosinolate		Selects the precursorMz corresponding to an MS2 signature (diagnostic neutral and ion losses)

Examples

java -cp ./assembly/pack.jar MainDistributionIntensityIons

java -cp ./assembly/pack.jar MainDistributionMzIons

java -cp ./assembly/pack.jar MainDistributionDiffMzIons -i 50000

ammonite example

Precursor Mz search

import $cp.`target/scala-2.13/mzXML-stream-assembly-1.0.jar`
import cats.effect.{IO, IOApp}
import fs2.{Stream, text, Pipe}
import fs2.io.file.{Files, Path}
import java.nio.file.Paths

import cats.effect.unsafe.implicits._
import fr.inrae.p2m2.mzxml._


val mzXMLFile = "./src/test/resources/LTQ_Orbitrap_precision32.mzXML"
val outputFile = "precursor_288p93.txt"


val formatPrecursorMz : Pipe[IO, Option[Seq[PrecursorMz]], String] = {
inStream =>
    inStream.map {
    case Some(p) => s"Precursor ${p.head.value} with precursorIntensity ${p.head.precursorIntensity} " +
        s"and precursorScanNum ${p.head.precursorScanNum}\n"
    case _ => ""
    }
}

SpectrumRequest(mzXMLFile).precursorMz(288.93,5000).map {
    case Some(r) => Some(r.precursorMz)
    case None => None
}
.filter(_.isDefined)
.through(formatPrecursorMz)
.through(text.utf8.encode)
.through(Files[IO].writeAll(Path(outputFile)))
.compile
.drain
.unsafeRunSync()

println(outputFile)

import $cp.`target/scala-2.13/mzXML-stream-assembly-1.0.jar`
import cats.effect.{IO, IOApp}
import fs2.{Stream, text, Pipe}
import fs2.io.file.{Files, Path}
import java.nio.file.Paths

import cats.effect.unsafe.implicits._
import fr.inrae.p2m2.mzxml._
import fr.inrae.p2m2.mzxml.utils.ChemicalConst

val mzXMLFile = "./src/test/resources/LTQ_Orbitrap_precision32.mzXML"
val deltaMp0Mp2     = 1.996 // Glucosinolate
val numberCarbonMin = 3
val numberCarbonMax = 35
val numberSulfurMin = 1.5
val numberSulfurMax = 5
val startTime = 0
val endTime = 5

{
  SpectrumRequest(mzXMLFile)
    .msLevel(1)
    .filter(_.isDefined)
    .map( _.get)
    .filter( _.retentionTimeInSeconds.getOrElse(0)>=startTime)
    .filter( _.retentionTimeInSeconds.getOrElse(Int.MaxValue)<=endTime)
    .map {
      (spectrum: Spectrum) => {
        spectrum.peaks.map {
            case (mz0, int0) =>
              val mz_ms_p2 = mz0 + deltaMp0Mp2
              val (mz1, int1) = spectrum.findClosestValueMz(mz0 + 1.0)
              val (mz2, int2) = spectrum.findClosestValueMz(mz_ms_p2)
              ((mz0, int0), (mz1, int1), (mz2, int2)) // isotopes

          }.filter {
            case (v0, v1, _) =>
              v1._2 >= v0._2 *
                (ChemicalConst.abundanceIsotope("C")(1) * numberCarbonMin +
                  ChemicalConst.abundanceIsotope("S")(1) * numberSulfurMin)

          }.filter {
            case (v0, v1, _) =>
              v1._2 < v0._2 *
                (ChemicalConst.abundanceIsotope("C")(1) * numberCarbonMax +
                  ChemicalConst.abundanceIsotope("S")(1) * numberSulfurMax)

          } /* criteria M2 of Isotope S are present 4.4 % */
          .filter {
            case (v0, _, v2) =>
              v2._2 >= v0._2 * ChemicalConst.abundanceIsotope("S")(2) * numberSulfurMin
          }
          .filter {
            case (v0, _, v2) =>
              v2._2 < v0._2 * ChemicalConst.abundanceIsotope("S")(2) * numberSulfurMax
          }.map(
            (spectrum.retentionTimeInSeconds.getOrElse(-1), _)
          )
      }
    }
    .map(x => x.map(y => y.toString()+"\n").mkString("\n"))
    .through(text.utf8.encode)
    .through(Files[IO].writeAll(Path(outputFile)))
    .compile
    .drain
    .unsafeRunSync()
}

amm example.sc

amm glucosinolateIons.sc ../mzxml-glucosinolate-analyser/src/test/resources/20181018-037.mzXML 100000