Timsrust 0.3.0

crates/sage-cli/src/main.rs

@@ -203,7 +203,7 @@ impl Runner {
             min_deisotope_mz.unwrap_or(0.0),
         );
 
-        let bruker_extensions = [".d", ".tdf", ".tdf_bin"];
+        let bruker_extensions = [".d", ".tdf", ".tdf_bin", "ms2", "raw"];
         let spectra = chunk
             .par_iter()
             .enumerate()
@@ -213,10 +213,16 @@ impl Runner {
                 let path_lower = path.to_lowercase();
                 let res = if path_lower.ends_with(".mgf.gz") || path_lower.ends_with(".mgf") {
                     sage_cloudpath::util::read_mgf(path, file_id)
-                } else if bruker_extensions
-                    .iter()
-                    .any(|ext| path_lower.ends_with(ext))
-                {
+                } else if bruker_extensions.iter().any(|ext| {
+                    if path_lower.ends_with(std::path::MAIN_SEPARATOR) {
+                        path_lower
+                            .strip_suffix(std::path::MAIN_SEPARATOR)
+                            .unwrap()
+                            .ends_with(ext)
+                    } else {
+                        path_lower.ends_with(ext)
+                    }
+                }) {
                     sage_cloudpath::util::read_tdf(path, file_id)
                 } else {
                     sage_cloudpath::util::read_mzml(path, file_id, sn)

crates/sage-cloudpath/Cargo.toml

@@ -23,7 +23,7 @@ log = "0.4.0"
 once_cell = "1.0"
 tokio = { version = "1.0", features = ["fs", "io-util", "rt", "macros"] }
 quick-xml = { version = "0.31.0", features = ["async-tokio"] }
-timsrust = "0.2.4"
+timsrust = "0.3.0"
 rayon = "1.5"
 reqwest = { version = "0.11", features = ["json", "rustls-tls"], default-features = false }
 regex = "1.6"

crates/sage-cloudpath/src/tdf.rs

@@ -1,5 +1,8 @@
 use rayon::prelude::*;
-use sage_core::spectrum::{Precursor, RawSpectrum, Representation};
+use sage_core::{
+    mass::Tolerance,
+    spectrum::{Precursor, RawSpectrum, Representation},
+};
 
 pub struct TdfReader;
 
@@ -9,21 +12,28 @@ impl TdfReader {
         path_name: impl AsRef<str>,
         file_id: usize,
     ) -> Result<Vec<RawSpectrum>, timsrust::Error> {
-        let dda_spectra: Vec<timsrust::Spectrum> =
-            timsrust::FileReader::new(path_name.as_ref())?.read_all_spectra();
-        let spectra: Vec<RawSpectrum> = (0..dda_spectra.len())
+        let spectrum_reader = timsrust::io::readers::SpectrumReader::new(path_name.as_ref());
+        let spectra: Vec<RawSpectrum> = (0..spectrum_reader.len())
             .into_par_iter()
             .map(|index| {
-                let dda_spectrum = &dda_spectra[index];
+                let dda_spectrum = spectrum_reader.get(index);
                 let mut precursor: Precursor = Precursor::default();
-                let dda_precursor: timsrust::Precursor =
-                    dda_spectrum.precursor.unwrap_as_precursor();
+                let dda_precursor: timsrust::ms_data::Precursor = dda_spectrum.precursor;
                 precursor.mz = dda_precursor.mz as f32;
-                precursor.charge = Option::from(dda_precursor.charge as u8);
-                // precursor.ion_mobility = Option::from(dda_precursor.im as f32);
-                precursor.intensity = Option::from(dda_precursor.intensity as f32);
+                precursor.charge = match dda_precursor.charge {
+                    Some(x) => Some(x as u8),
+                    None => None,
+                };
+                precursor.intensity = match dda_precursor.intensity {
+                    Some(x) => Some(x as f32),
+                    None => None,
+                };
                 precursor.spectrum_ref = Option::from(dda_precursor.frame_index.to_string());
                 precursor.inverse_ion_mobility = Option::from(dda_precursor.im as f32);
+                precursor.isolation_window = Option::from(Tolerance::Da(
+                    -dda_spectrum.isolation_width as f32 / 2.0,
+                    dda_spectrum.isolation_width as f32 / 2.0,
+                ));
                 let spectrum: RawSpectrum = RawSpectrum {
                     file_id,
                     precursors: vec![precursor],