Skip to content

Commit

Permalink
Unified identified peptide scan extraction
Browse files Browse the repository at this point in the history
  • Loading branch information
@douweschulte
douweschulte committed Oct 25, 2024
1 parent c26d0e9 commit 914f18c
Show file tree
Hide file tree
Showing 7 changed files with 233 additions and 195 deletions.
22 changes: 12 additions & 10 deletions examples/de-novo-align/src/main.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ use std::{collections::HashMap, fs::File, io::BufWriter};

use align::AlignScoring;
use clap::Parser;
use identification::SpectrumIds;
use itertools::Itertools;
use rayon::prelude::*;
use rustyms::{
Expand Down Expand Up @@ -75,10 +76,17 @@ fn main() {
HashMap::from([
("Peptide".to_string(), alignment.seq_b().to_string()),
(
"Rawfile".to_string(),
peptide
.raw_file()
.map_or(String::new(), |p| p.to_string_lossy().to_string()),
"Spectra ref".to_string(),
match peptide.scans() {
SpectrumIds::None => String::new(),
SpectrumIds::FileNotKnown(scans) => scans.iter().join(";"),
SpectrumIds::FileKnown(scans) => scans
.iter()
.map(|(file, scans)| {
format!("{}:{}", file.to_string_lossy(), scans.iter().join(";"))
})
.join("|"),
},
),
(
"De novo score".to_string(),
Expand Down Expand Up @@ -115,12 +123,6 @@ fn main() {
"Peptide length".to_string(),
peptide.peptide().map_or(0, |p| p.len()).to_string(),
),
(
"Scan".to_string(),
peptide
.scan_indices()
.map_or(String::new(), |s| s.into_iter().join(",")),
),
(
"Retention time".to_string(),
peptide
Expand Down
217 changes: 142 additions & 75 deletions rustyms/src/identification/identified_peptide.rs
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
use std::path::Path;
use std::path::PathBuf;

use itertools::Itertools;
use serde::{Deserialize, Serialize};

use super::{
Expand All @@ -12,7 +13,7 @@ use crate::{
};

/// A peptide that is identified by a de novo or database matching program
#[derive(Clone, PartialEq, Debug, Default, Serialize, Deserialize)]
#[derive(Clone, PartialEq, Debug, Serialize, Deserialize)]
pub struct IdentifiedPeptide {
/// The score -1.0..=1.0 if available in the original format
pub score: Option<f64>,
Expand All @@ -21,27 +22,24 @@ pub struct IdentifiedPeptide {
}

/// The definition of all special metadata for all types of identified peptides that can be read
#[derive(Clone, PartialEq, Debug, Default, Serialize, Deserialize)]
#[derive(Clone, PartialEq, Debug, Serialize, Deserialize)]
pub enum MetaData {
/// No metadata
#[default]
None,
/// Peaks metadata
Peaks(PeaksData),
/// Novor metadata
Novor(NovorData),
/// OPair metadata
Opair(OpairData),
/// Fasta metadata
Fasta(FastaData),
/// MaxQuant metadata
MaxQuant(MaxQuantData),
/// Sage metadata
Sage(SageData),
/// MSFragger metadata
MSFragger(MSFraggerData),
/// MSFragger metadata
/// mzTab metadata
MZTab(MZTabData),
/// Novor metadata
Novor(NovorData),
/// OPair metadata
Opair(OpairData),
/// Peaks metadata
Peaks(PeaksData),
/// Sage metadata
Sage(SageData),
}

impl IdentifiedPeptide {
Expand All @@ -56,7 +54,37 @@ impl IdentifiedPeptide {
| MetaData::MZTab(MZTabData { peptide, .. }) => Some(peptide),
MetaData::MSFragger(MSFraggerData { peptide, .. })
| MetaData::MaxQuant(MaxQuantData { peptide, .. }) => peptide.as_ref(),
MetaData::None => None,
}
}

/// Get the name of the format
pub const fn format_name(&self) -> &'static str {
match &self.metadata {
MetaData::Fasta(_) => "Fasta",
MetaData::MaxQuant(_) => "MaxQuant",
MetaData::MSFragger(_) => "MSFragger",
MetaData::MZTab(_) => "mzTab",
MetaData::Novor(_) => "Novor",
MetaData::Opair(_) => "OPair",
MetaData::Peaks(_) => "PEAKS",
MetaData::Sage(_) => "Sage",
}
}

/// Get the identifier
pub fn id(&self) -> String {
match &self.metadata {
MetaData::Peaks(PeaksData { scan, .. }) => scan.iter().join(";"),
MetaData::Novor(NovorData { id, scan, .. }) => id.unwrap_or(*scan).to_string(),
MetaData::Opair(OpairData { scan, .. }) => scan.to_string(),
MetaData::Sage(SageData { id, .. }) | MetaData::MZTab(MZTabData { id, .. }) => {
id.to_string()
}
MetaData::Fasta(FastaData { id, .. }) => id.clone(),
MetaData::MSFragger(MSFraggerData { scan, .. }) => scan.to_string(),
MetaData::MaxQuant(MaxQuantData { id, scan, .. }) => {
id.map_or_else(|| scan.iter().join(";"), |id| id.to_string())
}
}
}

Expand Down Expand Up @@ -86,7 +114,7 @@ impl IdentifiedPeptide {
| MetaData::MSFragger(MSFraggerData { z, .. })
| MetaData::MaxQuant(MaxQuantData { z, .. })
| MetaData::MZTab(MZTabData { z, .. }) => Some(*z),
MetaData::Fasta(_) | MetaData::None => None,
MetaData::Fasta(_) => None,
}
}

Expand All @@ -109,63 +137,50 @@ impl IdentifiedPeptide {
MetaData::MaxQuant(MaxQuantData { rt, .. })
| MetaData::Novor(NovorData { rt, .. })
| MetaData::MZTab(MZTabData { rt, .. }) => *rt,
MetaData::Fasta(_) | MetaData::None => None,
MetaData::Fasta(_) => None,
}
}

/// The scan indices of the spectrum for this identified peptide, if known.
pub fn scan_indices(&self) -> Option<Vec<usize>> {
/// The scans per rawfile that are at the basis for this identified peptide, if the rawfile is unknown there will be one
pub fn scans(&self) -> SpectrumIds {
match &self.metadata {
MetaData::Peaks(PeaksData { scan, .. }) => {
Some(scan.iter().flat_map(|i| &i.scans).copied().collect())
MetaData::Peaks(PeaksData { raw_file, scan, .. }) => raw_file.clone().map_or_else(
|| {
SpectrumIds::FileNotKnown(
scan.iter()
.flat_map(|s| s.scans.clone())
.map(SpectrumId::Index)
.collect(),
)
},
|raw_file| {
SpectrumIds::FileKnown(vec![(
raw_file,
scan.iter()
.flat_map(|s| s.scans.clone())
.map(SpectrumId::Index)
.collect(),
)])
},
),
MetaData::Novor(NovorData { scan, .. }) => {
SpectrumIds::FileNotKnown(vec![SpectrumId::Index(*scan)])
}
MetaData::Novor(NovorData { scan, .. }) | MetaData::Opair(OpairData { scan, .. }) => {
Some(vec![*scan])
MetaData::Opair(OpairData { raw_file, scan, .. }) => {
SpectrumIds::FileKnown(vec![(raw_file.clone(), vec![SpectrumId::Index(*scan)])])
}
MetaData::MaxQuant(MaxQuantData { scan_number, .. }) => Some(scan_number.clone()),
MetaData::MSFragger(MSFraggerData { spectrum, .. }) => Some(vec![spectrum.scan.0]),
MetaData::MZTab(MZTabData { spectra_ref, .. }) => Some(
spectra_ref
.iter()
.filter_map(|(_, _, id, _)| id.index())
.collect(),
),
MetaData::Sage(_) | MetaData::Fasta(_) | MetaData::None => None,
}
}

/// The native ids of the spectrum for this identified peptide, if known.
pub fn spectrum_native_ids(&self) -> Option<Vec<String>> {
match &self.metadata {
MetaData::Sage(SageData { native_id, .. }) => Some(vec![native_id.clone()]),
MetaData::MZTab(MZTabData { spectra_ref, .. }) => Some(
spectra_ref
.iter()
.filter_map(|(_, _, id, _)| id.native().map(ToString::to_string))
.collect(),
),
MetaData::MaxQuant(_)
| MetaData::Opair(_)
| MetaData::Novor(_)
| MetaData::Peaks(_)
| MetaData::Fasta(_)
| MetaData::MSFragger(_)
| MetaData::None => None,
}
}

/// Get the file name for the raw file
pub fn raw_file(&self) -> Option<&Path> {
match &self.metadata {
MetaData::Peaks(PeaksData { raw_file, .. }) => raw_file.as_deref(),
MetaData::Opair(OpairData { raw_file, .. })
| MetaData::MaxQuant(MaxQuantData { raw_file, .. })
| MetaData::Sage(SageData { raw_file, .. }) => Some(raw_file),
MetaData::MSFragger(MSFraggerData { spectrum, .. }) => Some(&spectrum.file),
MetaData::MZTab(MZTabData { spectra_ref, .. }) => {
spectra_ref.first().map(|r| r.0.as_path()) // TODO: Could contain multiple files
MetaData::MaxQuant(MaxQuantData { raw_file, scan, .. }) => {
SpectrumIds::FileKnown(vec![(
raw_file.clone(),
scan.iter().copied().map(SpectrumId::Index).collect(),
)])
}
MetaData::Novor(_) | MetaData::Fasta(_) | MetaData::None => None,
MetaData::MZTab(MZTabData { spectra_ref, .. }) => spectra_ref.clone(),
MetaData::MSFragger(MSFraggerData { raw_file, scan, .. })
| MetaData::Sage(SageData { raw_file, scan, .. }) => {
SpectrumIds::FileKnown(vec![(raw_file.clone(), vec![scan.clone()])])
}
MetaData::Fasta(_) => SpectrumIds::None,
}
}

Expand All @@ -186,7 +201,7 @@ impl IdentifiedPeptide {
}) => Some(MassOverCharge::new::<crate::system::mz>(
experimental_mass.value / (z.value as f64),
)),
MetaData::Fasta(_) | MetaData::None => None,
MetaData::Fasta(_) => None,
}
}

Expand All @@ -200,21 +215,19 @@ impl IdentifiedPeptide {
| MetaData::Sage(SageData { mass, .. }) => Some(*mass),
MetaData::MaxQuant(MaxQuantData { mass, .. }) => *mass,
MetaData::MZTab(MZTabData { mz, z, .. }) => mz.map(|mz| mz * z.to_float()),
MetaData::Fasta(_) | MetaData::None => None,
MetaData::Fasta(_) => None,
}
}

/// Get the absolute ppm error between the experimental and theoretical precursor mz
/// Get the absolute ppm error between the experimental and theoretical precursor mass
pub fn ppm_error(&self) -> Option<crate::system::Ratio> {
let exp_mz = self.experimental_mz()?;
let z = self.charge()?.to_float();
let mass = self
let exp_mass = self.experimental_mass()?;
let theo_mass = self
.peptide()
.and_then(|p| p.formulas().to_vec().pop())
.map(|f| f.monoisotopic_mass())?;
let theo_mz = mass / z;

Some(theo_mz.ppm(exp_mz))
Some(theo_mass.ppm(exp_mass))
}

/// Get the absolute mass error between the experimental and theoretical precursor mass
Expand All @@ -229,6 +242,60 @@ impl IdentifiedPeptide {
}
}

/// Multiple spectrum identifiers
#[derive(Clone, Default, PartialEq, Eq, Debug, Serialize, Deserialize)]
pub enum SpectrumIds {
/// When no spectra references are knwon at all
#[default]
None,
/// When the source file is now known
FileNotKnown(Vec<SpectrumId>),
/// When the source file is known, grouped per file
FileKnown(Vec<(PathBuf, Vec<SpectrumId>)>),
}

/// A spectrum identifier
#[derive(Clone, PartialEq, Eq, Debug, Serialize, Deserialize)]
pub enum SpectrumId {
/// A native id, the format differs between vendors
Native(String),
/// A spectrum index
Index(usize),
}

impl Default for SpectrumId {
fn default() -> Self {
Self::Index(0)
}
}

impl std::fmt::Display for SpectrumId {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
match self {
Self::Index(i) => write!(f, "{i}"),
Self::Native(n) => write!(f, "{n}"),
}
}
}

impl SpectrumId {
/// Get the index if this is an index
pub const fn index(&self) -> Option<usize> {
match self {
Self::Index(i) => Some(*i),
Self::Native(_) => None,
}
}

/// Get the native ID if this is a native ID
pub fn native(&self) -> Option<&str> {
match self {
Self::Index(_) => None,
Self::Native(n) => Some(n),
}
}
}

/// The required methods for any source of identified peptides
pub trait IdentifiedPeptideSource
where
Expand Down
10 changes: 5 additions & 5 deletions rustyms/src/identification/maxquant.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ format_family!(
MaxQuantVersion, [&MSMS, &MSMS_SCANS, &NOVO_MSMS_SCANS, &SILAC], b'\t';
required {
raw_file: PathBuf, |location: Location, _| Ok(Path::new(&location.get_string()).to_owned());
scan_number: Vec<usize>, |location: Location, _| location.or_empty().array(';').map(|s| s.parse(NUMBER_ERROR)).collect::<Result<Vec<usize>, CustomError>>();
scan: Vec<usize>, |location: Location, _| location.or_empty().array(';').map(|s| s.parse(NUMBER_ERROR)).collect::<Result<Vec<usize>, CustomError>>();
modifications: String, |location: Location, _| Ok(location.get_string());
proteins: String, |location: Location, _| Ok(location.get_string());
peptide: Option<LinearPeptide<SemiAmbiguous>>, |location: Location, custom_database: Option<&CustomDatabase>| location.or_empty().parse_with(|location| LinearPeptide::sloppy_pro_forma(
Expand Down Expand Up @@ -195,7 +195,7 @@ pub const MSMS: MaxQuantFormat = MaxQuantFormat {
rt: Some("retention time"),
scan_event_number: Some("scan event number"),
scan_index: Some("scan index"),
scan_number: "scan number",
scan: "scan number",
score_diff: Some("score diff"),
score: "score",
simple_mass_error_ppm: Some("simple mass error [ppm]"),
Expand Down Expand Up @@ -258,7 +258,7 @@ pub const MSMS_SCANS: MaxQuantFormat = MaxQuantFormat {
rt: Some("retention time"),
scan_event_number: Some("scan event number"),
scan_index: Some("scan index"),
scan_number: "scan number",
scan: "scan number",
score_diff: None,
score: "score",
simple_mass_error_ppm: None,
Expand Down Expand Up @@ -321,7 +321,7 @@ pub const NOVO_MSMS_SCANS: MaxQuantFormat = MaxQuantFormat {
rt: Some("retention time"),
scan_event_number: Some("scan event number"),
scan_index: Some("scan index"),
scan_number: "scan number",
scan: "scan number",
score_diff: None,
score: "score",
simple_mass_error_ppm: None,
Expand Down Expand Up @@ -384,7 +384,7 @@ pub const SILAC: MaxQuantFormat = MaxQuantFormat {
rt: Some("retention time"),
scan_event_number: None,
scan_index: None,
scan_number: "ms/ms scan numbers",
scan: "ms/ms scan numbers",
score_diff: None,
score: "score",
simple_mass_error_ppm: None,
Expand Down
Loading

0 comments on commit 914f18c

Please sign in to comment.