From a22de42bc93ad8438dcbb1e54da86cc22db3646d Mon Sep 17 00:00:00 2001
From: Kevin Velghe <kevin.velghe@ugent.be>
Date: Tue, 13 Aug 2024 16:42:40 +0200
Subject: [PATCH] use mz_read to read mgfs and mzmls

This add support for gziped files, without the need for us to implement
it.
---
 Cargo.toml          |  1 +
 src/lib.rs          |  2 +-
 src/parse_mzdata.rs | 21 +++++----------------
 3 files changed, 7 insertions(+), 17 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index d7fa121..f34b2b6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -12,3 +12,4 @@ crate-type = ["cdylib"]
 pyo3 = "0.20.0"
 mzdata = "0.20.0"
 timsrust = "0.3.0"
+mzpeaks = "0.17.0"
diff --git a/src/lib.rs b/src/lib.rs
index 61ee4d8..b78771b 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -40,7 +40,7 @@ pub fn get_ms2_spectra(spectrum_path: String) -> PyResult<Vec<ms2_spectrum::MS2S
 
     let spectra = match file_type {
         SpectrumFileType::MascotGenericFormat | SpectrumFileType::MzML => {
-            parse_mzdata::read_ms2_spectra(&spectrum_path, file_type)
+            parse_mzdata::read_ms2_spectra(&spectrum_path)
         }
         SpectrumFileType::BrukerRaw => parse_timsrust::read_ms2_spectra(&spectrum_path),
         // SpectrumFileType::ThermoRaw => parse_with_mzdata_thermo(&spectrum_path, file_type),
diff --git a/src/parse_mzdata.rs b/src/parse_mzdata.rs
index e11c805..5717d1a 100644
--- a/src/parse_mzdata.rs
+++ b/src/parse_mzdata.rs
@@ -3,6 +3,7 @@ use std::fs::File;
 
 use mzdata::io::{MGFReader, MzMLReader};
 use mzdata::params::ParamValue;
+use mzdata::mz_read;
 
 use crate::file_types::SpectrumFileType;
 use crate::ms2_spectrum::MS2Spectrum;
@@ -81,24 +82,12 @@ pub fn parse_precursor_info(
 /// Read MS2 spectra from spectrum files with mzdata
 pub fn read_ms2_spectra(
     spectrum_path: &str,
-    file_type: SpectrumFileType,
 ) -> Result<Vec<MS2Spectrum>, std::io::Error> {
-    let file = File::open(spectrum_path)?;
-    match file_type {
-        SpectrumFileType::MascotGenericFormat => Ok(MGFReader::new(file)
-            .map(MS2Spectrum::from)
-            .collect::<Vec<MS2Spectrum>>()),
-
-        SpectrumFileType::MzML => Ok(MzMLReader::new(file)
-            .filter(|spectrum| spectrum.description.ms_level == 2)
+    mz_read!(spectrum_path.as_ref(), reader => {
+        reader.filter(|spectrum| spectrum.description.ms_level == 2)
             .map(MS2Spectrum::from)
-            .collect::<Vec<MS2Spectrum>>()),
-
-        _ => Err(std::io::Error::new(
-            std::io::ErrorKind::InvalidInput,
-            "Unsupported file type for mzdata",
-        )),
-    }
+            .collect::<Vec<MS2Spectrum>>()
+    })
 }
 
 // pub fn parse_precursor_info_thermo(