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Merge pull request rusteomics#47 from aukeheerdink:NovoB
Implemented NovoB support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,165 @@ | ||
| use crate::{ | ||
| error::CustomError, | ||
| identification::{IdentifiedPeptide, IdentifiedPeptideSource, MetaData}, | ||
| modification::Ontology, | ||
| ontologies::CustomDatabase, | ||
| system::Ratio, | ||
| system::{usize::Charge, Mass}, | ||
| AminoAcid, LinearPeptide, SemiAmbiguous, SloppyParsingParameters, | ||
| }; | ||
|
|
||
| use serde::{Deserialize, Serialize}; | ||
|
|
||
| use super::{ | ||
| common_parser::Location, | ||
| csv::{parse_csv, CsvLine}, | ||
| BoxedIdentifiedPeptideIter, SequenceElement, | ||
| }; | ||
|
|
||
| use std::sync::OnceLock; | ||
|
|
||
| static NUMBER_ERROR: (&str, &str) = ( | ||
| "Invalid NovoB line", | ||
| "This column is not a number but it is required to be a number in this format", | ||
| ); | ||
|
|
||
| static PARAMETERS_LOCK: OnceLock<SloppyParsingParameters> = OnceLock::new(); | ||
|
|
||
| /// Global parsing parameters | ||
| #[allow(clippy::missing_panics_doc)] // These modifications exist | ||
| fn parameters() -> &'static SloppyParsingParameters { | ||
| PARAMETERS_LOCK.get_or_init(|| SloppyParsingParameters { | ||
| custom_alphabet: vec![ | ||
| ( | ||
| b's', | ||
| SequenceElement::new(AminoAcid::Serine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(21, None).unwrap()), | ||
| ), | ||
| ( | ||
| b't', | ||
| SequenceElement::new(AminoAcid::Tyrosine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(21, None).unwrap()), | ||
| ), | ||
| ( | ||
| b'y', | ||
| SequenceElement::new(AminoAcid::Threonine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(21, None).unwrap()), | ||
| ), | ||
| ( | ||
| b'n', | ||
| SequenceElement::new(AminoAcid::Asparagine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(7, None).unwrap()), | ||
| ), | ||
| ( | ||
| b'q', | ||
| SequenceElement::new(AminoAcid::Glutamine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(7, None).unwrap()), | ||
| ), | ||
| ( | ||
| b'C', | ||
| SequenceElement::new(AminoAcid::Cysteine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(6, None).unwrap()), | ||
| ), | ||
| ( | ||
| b'm', | ||
| SequenceElement::new(AminoAcid::Methionine.into(), None) | ||
| .with_simple_modification(Ontology::Unimod.find_id(35, None).unwrap()), | ||
| ), | ||
| ], | ||
| ..Default::default() | ||
| }) | ||
| } | ||
|
|
||
| format_family!( | ||
| /// The format for any NovoB file | ||
| NovoBFormat, | ||
| /// The data from any NovoB file | ||
| NovoBData, | ||
| NovoBVersion, [&NOVOB_V0_0_1], b'\t', Some(vec![ | ||
| "mcount".to_string(), | ||
| "charge".to_string(), | ||
| "pepmass".to_string(), | ||
| "senten".to_string(), | ||
| "delta_mass".to_string(), | ||
| "prob".to_string(), | ||
| "senten_reverse".to_string(), | ||
| "delta_mass_reverse".to_string(), | ||
| "prob_reverse".to_string() | ||
| ]); | ||
|
|
||
| required { | ||
| scan: usize, |location: Location, _| location.parse(NUMBER_ERROR); | ||
| z: Charge, |location: Location, _| location.parse::<usize>(NUMBER_ERROR).map(Charge::new::<crate::system::e>); | ||
| mass: Mass, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Mass::new::<crate::system::dalton>); | ||
|
|
||
| score_forward: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR); | ||
| ppm_diff_forward: Ratio, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Ratio::new::<crate::system::ratio::ppm>); | ||
| peptide_forward: LinearPeptide<SemiAmbiguous>, | location: Location, custom_database: Option<&CustomDatabase>| { | ||
| let location = location.trim_start_matches("['").trim_end_matches("']"); | ||
| LinearPeptide::sloppy_pro_forma( | ||
| location.full_line(), | ||
| location.location.clone(), | ||
| custom_database, | ||
| parameters(), | ||
| )}; | ||
|
|
||
| score_reverse: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR); | ||
| ppm_diff_reverse: Ratio, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Ratio::new::<crate::system::ratio::ppm>); | ||
| peptide_reverse: LinearPeptide<SemiAmbiguous>, | location: Location, custom_database: Option<&CustomDatabase>| { | ||
| let location = location.trim_start_matches("['").trim_end_matches("']"); | ||
| LinearPeptide::sloppy_pro_forma( | ||
| location.full_line(), | ||
| location.location.clone(), | ||
| custom_database, | ||
| parameters(), | ||
| )}; | ||
| } | ||
| optional { } | ||
| ); | ||
|
|
||
| impl From<NovoBData> for IdentifiedPeptide { | ||
| fn from(value: NovoBData) -> Self { | ||
| Self { | ||
| score: Some(value.score_forward.max(value.score_reverse)), | ||
| local_confidence: None, | ||
| metadata: MetaData::NovoB(value), | ||
| } | ||
| } | ||
| } | ||
|
|
||
| /// The only known version of NovoB | ||
| pub const NOVOB_V0_0_1: NovoBFormat = NovoBFormat { | ||
| version: NovoBVersion::V0_0_1, | ||
| scan: "mcount", | ||
| z: "charge", | ||
| mass: "pepmass", | ||
|
|
||
| score_forward: "prob", | ||
| peptide_forward: "senten", | ||
| ppm_diff_forward: "delta_mass", | ||
|
|
||
| score_reverse: "prob_reverse", | ||
| peptide_reverse: "senten_reverse", | ||
| ppm_diff_reverse: "delta_mass_reverse", | ||
| }; | ||
|
|
||
| /// All possible NovoB versions | ||
| #[derive(Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Default, Serialize, Deserialize)] | ||
| #[allow(non_camel_case_types)] | ||
| pub enum NovoBVersion { | ||
| #[default] | ||
| /// NovoB version 0.0.1 | ||
| V0_0_1, | ||
| } | ||
|
|
||
| impl std::fmt::Display for NovoBVersion { | ||
| fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::result::Result<(), std::fmt::Error> { | ||
| write!( | ||
| f, | ||
| "{}", | ||
| match self { | ||
| Self::V0_0_1 => "v0.0.1", | ||
| } | ||
| ) | ||
| } | ||
| } |
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