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ofilangiofilangi
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Merge pull request #3 from p2m2/test_gluco
Test gluco
2 parents ddf106d + 767896d commit 253963d

3 files changed

Lines changed: 118 additions & 64 deletions

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‎Readme.md‎

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Original file line numberDiff line numberDiff line change
@@ -64,6 +64,10 @@ java -cp ./assembly/pack.jar MainDistributionMzIons
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java -cp ./assembly/pack.jar MainDistributionDiffMzIons -i 50000
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```
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```bash
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java -cp ./assembly/pack.jar MainGlucosinolates src/test/resources/Orbitrap_Exploris_240_precision64.mzXML --output test.out --startRT 0 --endRT 2 --minIntensity 7500 --deltaMp0Mp2 1.9958 --carbonMin 3 --carbonMax 35 --sulfurMin 1.5 --sulfurMax 5 --precisionMz 0.0001
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```
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## ammonite example
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### Precursor Mz search

‎build.sbt‎

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Original file line numberDiff line numberDiff line change
@@ -36,15 +36,15 @@ ThisBuild / compile / javacOptions ++= Seq(
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libraryDependencies ++= Seq(
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"com.github.scopt" %% "scopt" % "4.1.0",
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"com.lucidchart" %% "xtract" % "2.3.0",
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"co.fs2" %% "fs2-core" % "3.9.2",
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"co.fs2" %% "fs2-io" % "3.9.2",
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"co.fs2" %% "fs2-core" % "3.9.2",
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"co.fs2" %% "fs2-core" % "3.11.0",
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"co.fs2" %% "fs2-io" % "3.11.0",
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"co.fs2" %% "fs2-core" % "3.11.0",
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"org.gnieh" %%"fs2-data-xml"%"1.8.0",
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"com.github.marklister" %% "base64" % "0.3.0",
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"com.github.nscala-time" %% "nscala-time" %"2.32.0",
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"org.scala-lang.modules" %% "scala-parallel-collections" % "1.0.4",
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"org.typelevel" %% "cats-effect-testing-utest" % "1.5.0" % Test,
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"com.lihaoyi" %% "utest" % "0.8.1" % Test,
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"com.github.nscala-time" %% "nscala-time" %"3.0.0",
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"org.scala-lang.modules" %% "scala-parallel-collections" % "1.2.0",
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"org.typelevel" %% "cats-effect-testing-utest" % "1.6.0" % Test,
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"com.lihaoyi" %% "utest" % "0.8.5" % Test,
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)
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testFrameworks += new TestFramework("utest.runner.Framework")

‎src/main/scala/MainGlucosinolates.scala‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,8 @@ import org.joda.time.format.PeriodFormat
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import scopt.OParser
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import scala.math._
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import cats.effect.kernel.Ref
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import cats.effect.unsafe.implicits.global
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object MainGlucosinolates extends IOApp {
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@@ -27,34 +29,57 @@ object MainGlucosinolates extends IOApp {
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private val builder = OParser.builder[Config]
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private val parser1 = {
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import builder._
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OParser.sequence(
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programName("MainGlucosinolates"),
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head("MainGlucosinolates", "1.0"),
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opt[String]('o', "output")
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.required()
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.action((x, c) => c.copy(outputFile = Some(x)))
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.text("Output file"),
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opt[Double]('s', "startRT")
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.optional()
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.action((x, c) => c.copy(startRT = Some(x)))
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.text("start RT"),
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opt[Double]('e', "endRT")
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.optional()
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.action((x, c) => c.copy(endRT = Some(x)))
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.text("end RT"),
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opt[Double]('i', "minIntensity")
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.optional()
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.action((x, c) => c.copy(minIntensity = x))
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.text("Minimum intensity threshold selecting the ions of interest"),
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arg[String]("<file>")
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.required()
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.action((x, c) => c.copy(mzFile = Some(x)))
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.text("Input mzXML file"),
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help("help").text("prints this usage text")
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)
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}
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import builder._
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OParser.sequence(
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programName("MainGlucosinolates"),
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head("MainGlucosinolates", "1.0"),
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opt[String]('o', "output")
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.required()
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.action((x, c) => c.copy(outputFile = Some(x)))
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.text("Output file"),
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opt[Double]('s', "startRT")
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.optional()
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.action((x, c) => c.copy(startRT = Some(x)))
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.text("Start retention time"),
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opt[Double]('e', "endRT")
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.optional()
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.action((x, c) => c.copy(endRT = Some(x)))
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.text("End retention time"),
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opt[Double]('i', "minIntensity")
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.optional()
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.action((x, c) => c.copy(minIntensity = x))
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.text("Minimum intensity threshold"),
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opt[Double]("deltaMp0Mp2")
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.optional()
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.action((x, c) => c.copy(deltaMp0Mp2 = x))
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.text("Delta between M0 and M2 peaks"),
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opt[Int]("carbonMin")
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.optional()
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.action((x, c) => c.copy(numberCarbonMin = x))
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.text("Minimum number of carbon atoms"),
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opt[Int]("carbonMax")
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.optional()
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.action((x, c) => c.copy(numberCarbonMax = x))
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.text("Maximum number of carbon atoms"),
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opt[Double]("sulfurMin")
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.optional()
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.action((x, c) => c.copy(numberSulfurMin = x))
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.text("Minimum number of sulfur atoms"),
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opt[Double]("sulfurMax")
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.optional()
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.action((x, c) => c.copy(numberSulfurMax = x))
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.text("Maximum number of sulfur atoms"),
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opt[Double]("precisionMz")
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.optional()
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.action((x, c) => c.copy(precisionMz = x))
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.text("Precision for m/z matching"),
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arg[String]("<file>")
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.required()
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.action((x, c) => c.copy(mzFile = Some(x)))
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.text("Input mzXML file"),
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help("help").text("prints this usage text")
81+
)
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}
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def run(args: List[String]): IO[ExitCode] = {
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OParser.parse(parser1, args, Config()) match {
6085
case Some(config) =>
@@ -63,54 +88,79 @@ object MainGlucosinolates extends IOApp {
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IO.raiseError(new IllegalArgumentException("Failed to parse arguments")).as(ExitCode.Error)
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}
6590
}
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67-
private def processFile(config: Config): IO[Unit] = {
91+
private def processFile(config: Config): IO[Unit] = {
6892
for {
6993
mzXMLFile <- IO.fromOption(config.mzFile)(new IllegalArgumentException("Missing mzXML file"))
7094
startTime = config.startRT.getOrElse(0.0)
7195
endTime = config.endRT.getOrElse(Double.MaxValue)
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processStart <- IO.realTime.map(rt => DateTime.now().plus(rt.toMillis))
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_ <- IO.println(s"Start analyze: $mzXMLFile")
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//resultsRef <-
75-
//Ref.of[IO, List[(Double, ((Double, Double), (Double, Double), (Double, Double)))]](List.empty)
76-
_ <- SpectrumRequest(mzXMLFile)
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100+
// Progress tracking
101+
progressRef <- Ref[IO].of(0)
102+
totalSpectraRef <- Ref[IO].of(0)
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104+
// First, count total spectra
105+
totalSpectra <- SpectrumRequest(mzXMLFile)
77106
.msLevel(1)
78107
.filter(_.isDefined)
79108
.map(_.get)
80-
81-
.map(s => {
82-
s.retentionTimeInSeconds.foreach(rt => println(f"RT: $rt%.2f"))
83-
s
84-
})
85-
.filter(s => s.retentionTimeInSeconds.exists(rt => rt >= startTime && rt <= endTime))
86-
.evalMap(spectrum => IO.blocking(processSpectrum(config, spectrum)))
87-
// .evalMap(results => resultsRef.update(_ ++ results))
88-
//.chunks
89-
//.mapAsync(4)(chunk => IO.cede *> IO.pure(chunk))
90-
.map(x => x.map(y => y.toString + "\n").mkString)
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.through(text.utf8.encode)
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.through(Files[IO].writeAll(Path(config.outputFile.getOrElse("output.txt"))))
109+
.filter(s => s.retentionTimeInSeconds.exists(rt => rt >= startTime && rt <= endTime))
93110
.compile
94-
.drain
111+
.count
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113+
_ <- totalSpectraRef.set(totalSpectra.toInt)
114+
115+
results <- SpectrumRequest(mzXMLFile)
116+
.msLevel(1)
117+
.filter(_.isDefined)
118+
.map(_.get)
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.filter(s => s.retentionTimeInSeconds.exists(rt => rt >= startTime && rt <= endTime))
120+
.evalMap { spectrum =>
121+
for {
122+
_ <- progressRef.update(_ + 1)
123+
current <- progressRef.get
124+
total <- totalSpectraRef.get
125+
_ <- IO.println(s"Progress: ${(current.toDouble / total * 100).round}% ($current/$total)")
126+
result <- IO.blocking(processSpectrum(config, spectrum))
127+
} yield result
128+
}
129+
.compile
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.toList
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97-
/*
98-
results <- resultsRef.get
99-
sortedResults = results.sortBy { case (_, ((mz0, _), _, _)) => -mz0 }
100-
_ <- IO.println(s"Sorting completed. Number of results: ${sortedResults.length}")
101-
_ <- Stream.emits(sortedResults)
102-
.evalMap(result => IO.println(result.toString))
132+
_ <- IO.println(s"Processing completed. Number of results: ${results.length}")
133+
sortedResults = results.flatten.sortBy { case (_, ((mz0, _), _, _)) => -mz0.toDouble }
134+
135+
_ <- IO.println(s"Sorting completed. Number of results: ${sortedResults.size}")
136+
137+
// CSV Header
138+
csvHeader = "RetentionTime;M0_mz;M0_intensity;M1_mz;M1_intensity;M2_mz;M2_intensity"
139+
140+
_ <- Stream.emits(Seq(csvHeader) ++ sortedResults)
141+
.map {
142+
case header: String => header
143+
case result: Product =>
144+
result match {
145+
case (rt: Double, ((mz0: Double, int0: Double), (mz1: Double, int1: Double), (mz2: Double, int2: Double))) =>
146+
s"$rt;$mz0;$int0;$mz1;$int1;$mz2;$int2"
147+
case _ => ""
148+
}
149+
}
150+
.map(_ + "\n")
151+
.through(text.utf8.encode)
152+
.through(Files[IO].writeAll(Path(config.outputFile.getOrElse("output.csv"))))
103153
.compile
104154
.drain
155+
105156
processEnd <- IO.realTime.map(rt => DateTime.now().plus(rt.toMillis))
106157
duration = new Interval(processStart, processEnd).toPeriod
107-
_ <- IO.println(s"Duration: ${PeriodFormat.getDefault.print(duration)}")*/
158+
_ <- IO.println(s"Duration: ${PeriodFormat.getDefault.print(duration)}")
159+
108160
} yield ()
109161
}
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111-
112-
113-
private def processSpectrum(config: Config, spectrum: Spectrum): Seq[(Double, ((Double, Double), (Double, Double), (Double, Double)))] = {
163+
private def processSpectrum(config: Config, spectrum: Spectrum): Seq[(Double, ((Double, Double), (Double, Double), (Double, Double)))] = {
114164
spectrum.peaks
115165
.filter { case (_, int0) => int0 > config.minIntensity }
116166
.flatMap { case (mz0, int0) =>

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