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inverse sample/metabolite in the input isocor file. #35

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merged 1 commit into from
Apr 1, 2022
Merged

inverse sample/metabolite in the input isocor file. #35

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4 changes: 2 additions & 2 deletions src/main/scala/fr/inrae/metabolomics/p2m2/converter/MassLynxOutput2IsocorInput.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,16 @@ case class MassLynxOutput2IsocorInput(
(field: CompoundField) => {
(compoundType match {
case "M+H" => Some(List(
sample,
field.Name,
sample,
correspondenceMetabolitesDerivative.getOrElse(field.Name,defaultDerivative),
0,
field.Area,
resolution.toString
).mkString("\t"))
case v if v.startsWith("M+") => Some(List(
sample,
field.Name,
sample,
correspondenceMetabolitesDerivative.getOrElse(field.Name,defaultDerivative),
v.replace("M+", "").toInt,
field.Area,
Expand Down
8 changes: 4 additions & 4 deletions src/test/scala/fr/inrae/metabolomics/p2m2/converter/MassLynxOutput2IsocorInputTest.scala
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Expand Up @@ -74,7 +74,7 @@ object MassLynxOutput2IsocorInputTest extends TestSuite {
header=OutputMassLynx.Header(),
results=MassLynxParser.parseResults(toParse.split("\n").toList)
)
assert( MassLynxOutput2IsocorInput(Map()).transform(entry) == List("M+H\tGlyN15_A_3\tACCQTAG\t0\t96688\t2000"))
assert( MassLynxOutput2IsocorInput(Map()).transform(entry) == List("GlyN15_A_3\tM+H\tACCQTAG\t0\t96688\t2000"))
}

test("basic run with a sample M+H, resolution=1000") {
Expand All @@ -90,7 +90,7 @@ object MassLynxOutput2IsocorInputTest extends TestSuite {
results=MassLynxParser.parseResults(toParse.split("\n").toList)
)
assert( MassLynxOutput2IsocorInput(Map(),resolution=1000).transform(entry) ==
List("M+H\tGlyN15_A_3\tACCQTAG\t0\t96688\t1000"))
List("GlyN15_A_3\tM+H\tACCQTAG\t0\t96688\t1000"))
}
test("basic run with a sample M+H, resolution=1000, defaultDerivative='TOTO'") {
val toParse =
Expand All @@ -106,7 +106,7 @@ object MassLynxOutput2IsocorInputTest extends TestSuite {
)

assert( MassLynxOutput2IsocorInput(Map(),resolution=1000, defaultDerivative="TOTO").transform(entry) ==
List("M+H\tGlyN15_A_3\tTOTO\t0\t96688\t1000"))
List("GlyN15_A_3\tM+H\tTOTO\t0\t96688\t1000"))
}

test("basic run with a sample M+H, resolution=1000, map( GlyN15_A_3 => 'TOTO')") {
Expand All @@ -123,7 +123,7 @@ object MassLynxOutput2IsocorInputTest extends TestSuite {
)

assert( MassLynxOutput2IsocorInput(Map("GlyN15_A_3" -> "TOTO"),resolution=1000).transform(entry) ==
List("M+H\tGlyN15_A_3\tTOTO\t0\t96688\t1000"))
List("GlyN15_A_3\tM+H\tTOTO\t0\t96688\t1000"))
}
}
}