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//! Code to handle the XL-MOD ontology
use context_error::{BoxedError, CreateError, FullErrorContent, StaticErrorContent};
use std::sync::Arc;
use thin_vec::ThinVec;
use mzcv::{
CVError, CVFile, CVSource, CVVersion, HashBufReader, OboOntology, OboStanzaType, OboValue,
};
use crate::{
chemistry::{DiagnosticIon, MolecularFormula},
ontology::{
Ontology,
ontology_modification::{ModData, OntologyModification},
},
sequence::{
LinkerSpecificity, PlacementRule, Position, SimpleModification, SimpleModificationInner,
},
};
/// XL-MOD modifications
#[allow(missing_copy_implementations, missing_debug_implementations)]
pub struct XlMod {}
impl CVSource for XlMod {
type Data = SimpleModificationInner;
type Structure = Vec<SimpleModification>;
fn cv_name() -> &'static str {
"XLMOD"
}
fn files() -> &'static [CVFile] {
&[CVFile {
name: "XLMOD",
extension: "obo",
url: Some("https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo"),
compression: mzcv::CVCompression::None,
}]
}
fn static_data() -> Option<(CVVersion, Self::Structure)> {
#[cfg(not(feature = "internal-no-data"))]
{
use bincode::config::Configuration;
let cache = bincode::decode_from_slice::<(CVVersion, Self::Structure), Configuration>(
include_bytes!("../databases/xlmod.dat"),
Configuration::default(),
)
.unwrap()
.0;
Some(cache)
}
#[cfg(feature = "internal-no-data")]
None
}
fn parse(
mut reader: impl Iterator<Item = HashBufReader<Box<dyn std::io::Read>, impl sha2::Digest>>,
) -> Result<(CVVersion, Self::Structure), Vec<BoxedError<'static, CVError>>> {
let reader = reader.next().unwrap();
OboOntology::from_raw(reader)
.map_err(|e| {
vec![
BoxedError::small(
CVError::FileCouldNotBeParsed,
e.get_short_description(),
e.get_long_description(),
)
.add_contexts(e.get_contexts().iter().cloned()),
]
})
.map(|obo| {
(obo.version(), {
let mut mods: Vec<SimpleModification> = Vec::new();
for obj in obo.objects {
if obj.stanza_type != OboStanzaType::Term {
continue;
}
let id = obj
.id
.1
.parse()
.expect("Incorrect XLMOD id, should be numerical");
let name = obj.lines["name"][0].0.clone();
let mut sites = None;
let mut length = None;
let mut mass = None;
let mut formula = None;
let mut origins = (Vec::new(), Vec::new());
let mut diagnostic_ions = Vec::new();
let description = obj
.definition
.as_ref()
.map_or_else(Box::default, |d| d.0.clone());
let cross_ids = obj
.definition
.as_ref()
.map_or_else(ThinVec::new, |d| d.1.clone().into());
let synonyms = obj
.synonyms
.iter()
.map(|s| (s.scope, s.synonym.clone()))
.collect();
for (id, value) in &obj.property_values {
match id.as_ref() {
"reactionSites" => {
sites = if let OboValue::Integer(n) = value[0].0 {
Some(u8::try_from(n).unwrap())
} else {
dbg!(obj);
unreachable!()
}
}
"spacerLength" => {
length = if let OboValue::Float(n) = value[0].0 {
Some(ordered_float::OrderedFloat(n))
} else {
None // can contain ranges
}
}
"monoIsotopicMass" => {
mass = if let OboValue::Float(n) = value[0].0 {
Some(ordered_float::OrderedFloat(n))
} else {
dbg!(obj);
unreachable!()
}
}
"deadEndFormula" => {
sites = Some(1);
formula = Some(
MolecularFormula::xlmod(&value[0].0.to_string()).unwrap(),
);
}
"bridgeFormula" => {
sites = Some(2);
formula = Some(
MolecularFormula::xlmod(&value[0].0.to_string()).unwrap(),
);
}
"specificities" => {
// specificities: "(C,U)" xsd:string
// specificities: "(K,N,Q,R,Protein N-term)&(E,D,Protein C-term)" xsd:string
if let Some((l, r)) = value[0].0.to_string().split_once('&') {
origins = (
l.trim_matches(['(', ')'])
.split(',')
.map(|s| s.trim().to_string())
.collect(),
r.trim_matches(['(', ')'])
.split(',')
.map(|s| s.trim().to_string())
.collect(),
);
} else {
origins = (
value[0]
.0
.to_string()
.trim_matches(['(', ')'])
.split(',')
.map(|s| s.trim().to_string())
.collect(),
Vec::new(),
);
}
}
"secondarySpecificities" => {
// secondarySpecificities: "(S,T,Y)" xsd:string
origins.0.extend(
value[0]
.0
.to_string()
.trim_matches(['(', ')'])
.split(',')
.map(|s| s.trim().to_string()),
);
}
"reporterMass" | "CID_Fragment" => {
// reporterMass: "555.2481" xsd:double
// CID_Fragment: "828.5" xsd:double
diagnostic_ions.push(DiagnosticIon(
MolecularFormula::with_additional_mass(
if let OboValue::Float(n) = value[0].0 {
n
} else {
dbg!(obj);
unreachable!()
},
),
));
}
_ => {}
}
}
let origins = (
read_placement_rules(&origins.0),
read_placement_rules(&origins.1),
);
if let Some(mass) = mass {
// Ignore the mass if a formula is set
if formula.is_none() {
formula = Some(MolecularFormula::with_additional_mass(mass.0));
}
}
if sites == Some(2) || !origins.1.is_empty() {
mods.push(
OntologyModification {
formula: formula.unwrap_or_default(),
name,
description,
cross_ids,
synonyms,
id,
ontology: Ontology::Xlmod,
obsolete: obj.obsolete,
data: ModData::Linker {
length,
specificities: vec![if origins.1.is_empty() {
LinkerSpecificity::Symmetric {
rules: origins.0,
stubs: Vec::new(),
neutral_losses: Vec::new(),
diagnostic: diagnostic_ions,
}
} else {
LinkerSpecificity::Asymmetric {
rules: (origins.0, origins.1),
stubs: Vec::new(),
neutral_losses: Vec::new(),
diagnostic: diagnostic_ions,
}
}],
},
}
.into(),
);
} else if sites == Some(3) {
// Ignore
} else {
mods.push(Arc::new(
OntologyModification {
formula: formula.unwrap_or_default(),
name,
description,
cross_ids,
synonyms,
ontology: Ontology::Xlmod,
obsolete: obj.obsolete,
id,
data: ModData::Mod {
specificities: vec![(
origins.0,
Vec::new(),
diagnostic_ions,
)],
},
}
.into(),
));
}
}
mods
})
})
}
}
fn read_placement_rules(bricks: &[String]) -> Vec<PlacementRule> {
if bricks.is_empty() {
vec![PlacementRule::Anywhere]
} else {
bricks
.iter()
.filter_map(|brick| {
if brick.len() == 1 {
Some(PlacementRule::AminoAcid(
vec![brick.try_into().unwrap()].into(),
Position::Anywhere,
))
} else if *brick == "Protein N-term" {
Some(PlacementRule::Terminal(Position::ProteinNTerm))
} else if *brick == "Protein C-term" {
Some(PlacementRule::Terminal(Position::ProteinCTerm))
} else if ["Thy"].contains(&brick.as_str()) {
None
} else {
panic!("Invalid placement rule: '{brick}'")
}
})
.collect()
}
}