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fix parsing precursor charge in MGF files #13

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merged 3 commits into from
Oct 31, 2024
Merged

fix parsing precursor charge in MGF files #13

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fe44c6c
fix parsing precursor charge in MGF files
paretje Oct 23, 2024
d54040f
don't overwrite charge if it was already set
paretje Oct 24, 2024
edc09dc
add mgf test case
paretje Oct 24, 2024
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92 changes: 45 additions & 47 deletions src/io/mgf.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,7 @@ struct SpectrumBuilder<
pub intensity_array: Vec<f32>,
pub charge_array: Vec<i32>,
pub has_charge: u32,
pub precursor_charge: Option<i32>,
pub detail_level: DetailLevel,
empty_metadata: bool,
centroided_type: PhantomData<C>,
Expand All @@ -114,6 +115,7 @@ impl<C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> Default for SpectrumB
intensity_array: Default::default(),
charge_array: Default::default(),
has_charge: Default::default(),
precursor_charge: Default::default(),
detail_level: Default::default(),
centroided_type: Default::default(),
deconvoluted_type: Default::default(),
Expand Down Expand Up @@ -341,17 +343,8 @@ impl<R: io::Read, C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> MGFReade
.map_err(|e| warn!("Failed to parse PEPMASS intensity {value}: {e}"))
.unwrap_or_default();
let charge: Option<i32> = match parts.next() {
Some(c) => match c.parse::<i32>() {
Ok(val) => Some(val),
Err(e) => {
self.state = MGFParserState::Error;
self.error = Some(MGFError::MalformedHeaderLine(format!(
"Malformed charge value in PEPMASS header {value}: {e}"
)));
return false;
}
},
None => None,
Some(c) => self.parse_charge(c),
None => builder.precursor_charge,
};
builder.description.precursor = Some(Precursor {
ions: vec![SelectedIon {
Expand All @@ -364,40 +357,16 @@ impl<R: io::Read, C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> MGFReade
});
}
"CHARGE" => {
let (sign, value, tail_sign) = if let Some(stripped) = value.strip_suffix('+') {
(1, stripped, true)
} else if let Some(stripped) = value.strip_suffix('-') {
(-1, stripped, true)
} else {
(1, value, false)
};

if tail_sign && (value.starts_with('-') || value.starts_with('+')) {
self.state = MGFParserState::Error;
self.error = Some(MGFError::MalformedHeaderLine(format!(
"Could not parse CHARGE header {value}"
)));
return false;
}

match value.parse::<i32>() {
Ok(z) => {
if let Some(ion) = builder
.description
.precursor
.get_or_insert_with(Precursor::default)
.iter_mut()
.last()
{
ion.charge = Some(sign * z);
}
}
Err(e) => {
self.state = MGFParserState::Error;
self.error = Some(MGFError::MalformedHeaderLine(format!(
"Could not parse CHARGE header {value} : {e}"
)));
return false;
builder.precursor_charge = self.parse_charge(value);
if let Some(ion) = builder
.description
.precursor
.get_or_insert_with(Precursor::default)
.iter_mut()
.last()
{
if ion.charge.is_none() {
ion.charge = builder.precursor_charge
}
}
}
Expand All @@ -418,6 +387,35 @@ impl<R: io::Read, C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> MGFReade
}
}

fn parse_charge(&mut self, value: &str) -> Option<i32> {
let (sign, value, tail_sign) = if let Some(stripped) = value.strip_suffix('+') {
(1, stripped, true)
} else if let Some(stripped) = value.strip_suffix('-') {
(-1, stripped, true)
} else {
(1, value, false)
};

if tail_sign && (value.starts_with('-') || value.starts_with('+')) {
self.state = MGFParserState::Error;
self.error = Some(MGFError::MalformedHeaderLine(format!(
"Could not parse charge value {value}"
)));
return None;
}

match value.parse::<i32>() {
Ok(z) => Some(sign * z),
Err(e) => {
self.state = MGFParserState::Error;
self.error = Some(MGFError::MalformedHeaderLine(format!(
"Could not parse charge value {value} : {e}"
)));
return None;
}
}
}

fn handle_peak(&mut self, line: &str, builder: &mut SpectrumBuilder<C, D>) -> bool {
let peak_line = self.parse_peak_from_line(line, builder).unwrap_or(false);
if peak_line {
Expand Down Expand Up @@ -1197,7 +1195,7 @@ mod test {
}
}
assert_eq!(ms1_count, 0);
assert_eq!(msn_count, 34);
assert_eq!(msn_count, 35);
}

#[test]
Expand All @@ -1224,7 +1222,7 @@ mod test {
})
}
assert_eq!(ms1_count, 0);
assert_eq!(msn_count, 34);
assert_eq!(msn_count, 35);
}

#[test]
Expand Down
2 changes: 1 addition & 1 deletion src/io/shorthand.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -310,7 +310,7 @@ mod test {
assert_eq!(val.len(), 48);
let val: Vec<_> =
mz_read!("./test/data/small.mgf".as_ref(), reader => { reader.collect() })?;
assert_eq!(val.len(), 34);
assert_eq!(val.len(), 35);
let val = mz_read!("./test/data/small.mzML".as_ref(), reader => { reader.file_description().clone() })?;
assert_eq!(val.source_files.len(), 1);
Ok(())
Expand Down
13 changes: 13 additions & 0 deletions test/data/small.mgf
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Original file line number Diff line number Diff line change
Expand Up @@ -25514,3 +25514,16 @@ PEPMASS=882.535034179688 29807.576171875
1743.361206 3.1923613548
END IONS

BEGIN IONS
TITLE=charge before pepmass
CHARGE=2+
PEPMASS=475.137295
ION_MOBILITY=42.42
RTINSECONDS=51.2
72.04439 100
148.06043 600
232.07504 300
263.08737 400
347.10198 500
423.11802 200
END IONS
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