rustyms 0.10.0

A library to handle proteomic mass spectrometry data and match peptides to spectra.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110

use crate::{
    error::CustomError,
    identification::{
        common_parser::{OptionalColumn, OptionalLocation},
        IdentifiedPeptide, IdentifiedPeptideSource, MetaData,
    },
    ontologies::CustomDatabase,
    system::{isize::Charge, MassOverCharge, Time},
    Peptidoform, SemiAmbiguous,
};

use std::path::{Path, PathBuf};

use serde::{Deserialize, Serialize};

use super::{
    common_parser::Location,
    csv::{parse_csv, CsvLine},
    BoxedIdentifiedPeptideIter,
};

static NUMBER_ERROR: (&str, &str) = (
    "Invalid SpectrumSequenceList line",
    "This column is not a number but it is required to be a number in this format",
);

format_family!(
    /// The format for any [SSL file](https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats).
    SpectrumSequenceListFormat,
    /// The data from any SSL file
    SpectrumSequenceListData,
    SpectrumSequenceListVersion, [&SSL], b'\t', None;
    required {
        raw_file: PathBuf, |location: Location, _| Ok(Path::new(&location.get_string()).to_owned());
        scan: usize, |location: Location, _| location.parse(NUMBER_ERROR);
        z: Charge, |location: Location, _| location

            .trim_end_matches(".0")
            .parse::<isize>(NUMBER_ERROR)
            .map(Charge::new::<crate::system::e>);
    }
    optional {
        start_time: Time, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Time::new::<crate::system::time::min>);
        end_time: Time, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Time::new::<crate::system::time::min>);
        peptide: Peptidoform<SemiAmbiguous>, |location: Location, custom_database: Option<&CustomDatabase>| Peptidoform::pro_forma(location.as_str(), custom_database).map(|p|p.into_semi_ambiguous().unwrap());
        score: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
        score_type: String, |location: Location, _| Ok(location.get_string());
        rt: Time, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(Time::new::<crate::system::time::min>);
        adduct: String, |location: Location, _| Ok(location.get_string());
        precursormz: MassOverCharge, |location: Location, _| location.parse::<f64>(NUMBER_ERROR).map(MassOverCharge::new::<crate::system::mz>);
        moleculename: String, |location: Location, _| Ok(location.get_string());
        inchikey: String, |location: Location, _| Ok(location.get_string());
        otherkeys: String, |location: Location, _| Ok(location.or_empty().get_string());
        ion_mobility: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
        ion_mobility_units: String, |location: Location, _| Ok(location.get_string());
        ccs: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
    }
);

impl From<SpectrumSequenceListData> for IdentifiedPeptide {
    fn from(value: SpectrumSequenceListData) -> Self {
        Self {
            score: value.score,
            local_confidence: None,
            metadata: MetaData::SpectrumSequenceList(value),
        }
    }
}

/// General type of SSL files
pub const SSL: SpectrumSequenceListFormat = SpectrumSequenceListFormat {
    version: SpectrumSequenceListVersion::SSL,
    raw_file: "file",
    scan: "scan",
    z: "charge",
    start_time: OptionalColumn::Optional("start-time"),
    end_time: OptionalColumn::Optional("end-time"),
    peptide: OptionalColumn::Optional("sequence"),
    score: OptionalColumn::Optional("score"),
    score_type: OptionalColumn::Optional("score-type"),
    rt: OptionalColumn::Optional("retention-time"),
    adduct: OptionalColumn::Optional("adduct"),
    precursormz: OptionalColumn::Optional("precursorMZ"),
    moleculename: OptionalColumn::Optional("moleculename"),
    inchikey: OptionalColumn::Optional("inchikey"),
    otherkeys: OptionalColumn::Optional("otherkeys"),
    ion_mobility: OptionalColumn::Optional("ion-mobility"),
    ion_mobility_units: OptionalColumn::Optional("ion-mobility-units"),
    ccs: OptionalColumn::Optional("ccs"),
};

/// All possible SpectrumSequenceList versions
#[derive(Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Default, Serialize, Deserialize)]
#[expect(clippy::upper_case_acronyms)]
pub enum SpectrumSequenceListVersion {
    #[default]
    /// SSL file format
    SSL,
}

impl std::fmt::Display for SpectrumSequenceListVersion {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::result::Result<(), std::fmt::Error> {
        write!(
            f,
            "{}",
            match self {
                Self::SSL => "",
            }
        )
    }
}