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Merge pull request rusteomics#51 from aukeheerdink/Cascadia-support
Implemented Cascadia support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| use crate::{ | ||
| error::CustomError, | ||
| identification::{ | ||
| common_parser::{OptionalColumn, OptionalLocation}, | ||
| IdentifiedPeptide, IdentifiedPeptideSource, MetaData, | ||
| }, | ||
| ontologies::CustomDatabase, | ||
| system::{isize::Charge, MassOverCharge, Time}, | ||
| LinearPeptide, 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 | ||
| 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: LinearPeptide<SemiAmbiguous>, |location: Location, custom_database: Option<&CustomDatabase>| LinearPeptide::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)] | ||
| #[allow(non_camel_case_types)] | ||
| 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 => "", | ||
| } | ||
| ) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| #![allow(clippy::missing_panics_doc)] | ||
| use std::io::BufReader; | ||
|
|
||
| use crate::identification::{test_format, SpectrumSequenceListData, SpectrumSequenceListVersion}; | ||
|
|
||
| #[test] | ||
| fn cascadia_v0_0_5() { | ||
| match test_format::<SpectrumSequenceListData>( | ||
| BufReader::new(CASCADIA_V0_0_5.as_bytes()), | ||
| None, | ||
| false, | ||
| false, | ||
| Some(SpectrumSequenceListVersion::SSL), | ||
| ) { | ||
| Ok(n) => assert_eq!(n, 20), | ||
| Err(e) => { | ||
| println!("{e}"); | ||
| panic!("Failed identified peptides test"); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| #[test] | ||
| fn small_molecule_example() { | ||
| match test_format::<SpectrumSequenceListData>( | ||
| BufReader::new(SMALL_MOLECULES_EXAMPLE.as_bytes()), | ||
| None, | ||
| false, | ||
| false, | ||
| Some(SpectrumSequenceListVersion::SSL), | ||
| ) { | ||
| Ok(n) => assert_eq!(n, 6), | ||
| Err(e) => { | ||
| println!("{e}"); | ||
| panic!("Failed identified peptides test"); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| #[test] | ||
| fn peptide_example() { | ||
| match test_format::<SpectrumSequenceListData>( | ||
| BufReader::new(PEPTIDE_EXAMPLE.as_bytes()), | ||
| None, | ||
| true, | ||
| false, | ||
| Some(SpectrumSequenceListVersion::SSL), | ||
| ) { | ||
| Ok(n) => assert_eq!(n, 12), | ||
| Err(e) => { | ||
| println!("{e}"); | ||
| panic!("Failed identified peptides test"); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| const CASCADIA_V0_0_5: &str = "file scan charge sequence score-type score retention-time start-time end-time | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 140 4.0 VNHKPSNTKVDKK Cascadia Score 0.8716757 13.830939 13.700380273173717 13.961498312641712 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 143 4.0 LANVNHKPSNTKVDK Cascadia Score 0.9688815 13.73074 13.600180573771862 13.861298613239857 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 284 4.0 LANVNHKPSNTKVDK Cascadia Score 0.91546655 14.112868 13.982309289286999 14.243427328754994 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 350 4.0 TYLANVNHKPSNTK Cascadia Score 0.9532166 14.182865 14.052306123088268 14.313424162556263 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 374 4.0 KENAGEDPGLARQAPKPR Cascadia Score 0.9884338 14.223199 14.092639870952038 14.353757910420033 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 428 4.0 LANVNHKPSNTKVDK Cascadia Score 0.8682205 14.452167 14.321607537578014 14.58272557704601 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 559 3.0 LTPPSREEMTK Cascadia Score 0.94662637 14.79058 14.660020776103405 14.9211388155714 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 624 2.0 KDVDQYMTK Cascadia Score 0.9709009 14.849122 14.718563027690319 14.979681067158314 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 832 3.0 LTPPSREEMTK Cascadia Score 0.98843235 15.338381 15.207821793864635 15.46893983333263 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 939 2.0 YVDGVEVHNAK Cascadia Score 0.8673074 15.534778 15.40421862156239 15.665336661030384 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1003 3.0 KAVGGLGKLGKDA Cascadia Score 0.91004914 15.7533655 15.6228064969286 15.883924536396595 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1064 4.0 HKVYASEVTHQGLSSPVTK Cascadia Score 0.98483497 15.964101 15.833541817973522 16.094659857441517 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1189 3.0 QAPGKGLESVAR Cascadia Score 0.91872495 16.191717 16.06115812809315 16.322276167561146 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1195 3.0 LTPPSREEMTK Cascadia Score 0.9785851 16.206034 16.07547468693104 16.336592726399036 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1212 2.0 KVLPVPQK Cascadia Score 0.9976683 16.322432 16.191872544597057 16.452990584065052 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1219 3.0 EVTHQGLSSPVTK Cascadia Score 0.99756336 16.327246 16.196686692546276 16.45780473201427 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1320 2.0 LTVDGVSR Cascadia Score 0.97489554 16.50676 16.37620062382069 16.637318663288685 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1339 3.0 LTPPSREEMTK Cascadia Score 0.9637745 16.652891 16.52233213932362 16.783450178791615 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 26981 4.0 THTC[Carbamidomethyl]PPC[Carbamidomethyl]PAPELLGGPSVFLFPPKPK Cascadia Score 0.85148484 75.06698 74.93641943485585 75.19753747432384 | ||
| ../test_data/test/20230408_F1_UM4_Peng0013_SA_EXT00_her_01_tryp.mzML 1397 4.0 HKVYAGEVTHQGLSSPVTK Cascadia Score 0.99907994 16.68329 16.552731461833385 16.81384950130138"; | ||
|
|
||
| const SMALL_MOLECULES_EXAMPLE: &str = r#"file scan charge adduct inchikey chemicalformula moleculename otherkeys | ||
| dexcaf_051017.mzML 01369 -1 [M-H] ZXPLRDFHBYIQOX-BTBVOZEKSA-N C24H44O21N0 Glc04Reduced | ||
| dexcaf_051017.mzML 01639 -1 [M-H] NBVGBCYERZIRIP-JAMOUWTMSA-N C30H54O26N0 Glc05Reduced | ||
| dexcaf_051017.mzML 01855 -1 [M-H] PNHJKLJIDNHXFR-ZGJYWSOBSA-N C36H64O31N0 Glc06Reduced | ||
| dexcaf_051017.mzML 02029 -1 [M-H] NVKJDLBVRSXYRE-BMFDHOHESA-N C42H74O36N0 Glc07Reduced | ||
| dexcaf_051017.mzML 02179 -1 [M-H] YMRGEPQWJZHXFF-MGQBKJSVSA-N C48H84O41N0 Glc08Reduced | ||
| dexcaf_051017.mzML 01079 -1 [M-H] RYYVLZVUVIJVGH-UHFFFAOYSA-N C8H10N4O2 Caffeine "InChI:1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 HMDB:01847 CAS:58-08-2 SMILES:Cn1cnc2n(C)c(=O)n(C)c(=O)c12""#; | ||
|
|
||
| const PEPTIDE_EXAMPLE: &str = "file scan charge sequence | ||
| demo.ms2 8 3 VGAGAPVYLAAVLEYLAAEVLELAGNAAR | ||
| demo.ms2 1806 2 LAESITIEQGK | ||
| demo.ms2 2572 2 ELAEDGC[+57.0]SGVEVR | ||
| demo.ms2 3088 2 TTAGAVEATSEITEGK | ||
| demo.ms2 3266 2 DC[+57.0]EEVGADSNEGGEEEGEEC[+57.0] | ||
| demo.ms2 9734 3 IWELEFPEEAADFQQQPVNAQ[-17.0]PQN | ||
| demo.ms2 20919 3 VHINIVVIGHVDSGK | ||
| ../elsewhere/spec.mzXML 00497 2 LKEPAQNTADNAK | ||
| ../elsewhere/spec.mzXML 00680 2 ALEGPGPGEDAAHSENNPPR | ||
| ../elsewhere/spec.mzXML 00965 2 FFSHEAEQK | ||
| ../elsewhere/spec.mzXML 01114 2 C[+57.0]GPSQPLK | ||
| ../elsewhere/spec.mzXML 01382 2 AVHVQVTDAEAGK"; |