MaldiAMRKit 0.19.0__tar.gz → 0.20.0__tar.gz

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0/MaldiAMRKit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MaldiAMRKit
-Version: 0.19.0
+Version: 0.20.0
 Summary: A comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes
 Author-email: Ettore Rocchi <ettore.rocchi3@unibo.it>
 License-Expression: MIT
@@ -52,6 +52,11 @@ Requires-Dist: hypothesis>=6.0.0; extra == "dev"
 Provides-Extra: batch
 Requires-Dist: umap-learn>=0.5; extra == "batch"
 Requires-Dist: combatlearn>=1.3; extra == "batch"
+Provides-Extra: formats
+Requires-Dist: pyteomics>=4.0; extra == "formats"
+Requires-Dist: lxml>=4.0; extra == "formats"
+Requires-Dist: psims>=1.0; extra == "formats"
+Requires-Dist: pynumpress>=0.1.5; python_version >= "3.11" and extra == "formats"
 Dynamic: license-file
 
 # MaldiAMRKit
@@ -108,6 +113,14 @@ pip install maldiamrkit[batch]
 
 Installs [`combatlearn`](https://github.com/EttoreRocchi/combatlearn) for ComBat-based batch effect correction and `umap-learn` for UMAP exploratory plots.
 
+### Optional: extended mzML/mzXML support
+
+```bash
+pip install maldiamrkit[formats]
+```
+
+`.mzML` and `.mzXML` files are read out of the box (zlib-compressed or uncompressed arrays). This extra installs [`pyteomics`](https://pyteomics.readthedocs.io/) with `lxml`, `psims`, and `pynumpress`, which additionally handle numpress-compressed arrays. `pynumpress` ships no wheels for Python 3.10, so numpress arrays need Python 3.11 or newer.
+
 ### Development Installation
 
 ```bash
@@ -160,9 +173,10 @@ pip install -e .[dev]
 - **Dataset Building & Loading**: `DatasetBuilder` and `DatasetLoader` with pluggable layout adapters (`FlatLayout`, `BrukerTreeLayout`, `DRIAMSLayout`, `MARISMaLayout`)
 - **Replicate Collapsing**: `DRIAMSLayout(collapse_replicates=True)` merges technical replicates (`_MALDI<N>`) to one row per isolate at load time via the active `duplicate_strategy`
 - **Bruker Format Support**: Read Bruker flexAnalysis binary data (fid/1r + acqus) natively via `read_spectrum()` on directories
+- **Open Formats**: Read `.mzML` and `.mzXML` files (optionally gzipped) via `read_spectrum()`, `MaldiSpectrum`, and `FlatLayout(spectrum_ext=".mzML")`; `pip install maldiamrkit[formats]` adds `pyteomics` for numpress-compressed arrays
 - **MIC Parsing**: `parse_mic_column()` for parsing MIC strings with qualifiers and European decimals
 - **Composable Filters**: `SpeciesFilter`, `DrugFilter`, `QualityFilter`, `MetadataFilter` combinable with `&`/`|`/`~` operators
-- **Spectrum Export**: Save spectra to CSV or TXT via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
+- **Spectrum Export**: Save spectra to CSV, TXT, or mzML via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
 
 ### Visualization & Tools
 - **Exploratory Plots**: PCA, t-SNE, and UMAP scatter plots colored by species, resistance phenotype, or any metadata column

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/MaldiAMRKit.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 requirements-batch.txt
 requirements-dev.txt
 requirements-docs.txt
+requirements-formats.txt
 requirements.txt
 MaldiAMRKit.egg-info/PKG-INFO
 MaldiAMRKit.egg-info/SOURCES.txt
@@ -72,6 +73,7 @@ maldiamrkit/evaluation/splitting.py
 maldiamrkit/io/__init__.py
 maldiamrkit/io/mic.py
 maldiamrkit/io/readers.py
+maldiamrkit/io/writers.py
 maldiamrkit/preprocessing/__init__.py
 maldiamrkit/preprocessing/binning.py
 maldiamrkit/preprocessing/merging.py

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/MaldiAMRKit.egg-info/requires.txt

@@ -31,3 +31,11 @@ sphinx-design>=0.6.0
 sphinxcontrib-typer>=0.5.0
 nbsphinx>=0.9.0
 ipykernel>=6.0.0
+
+[formats]
+pyteomics>=4.0
+lxml>=4.0
+psims>=1.0
+
+[formats:python_version >= "3.11"]
+pynumpress>=0.1.5

{maldiamrkit-0.19.0/MaldiAMRKit.egg-info → maldiamrkit-0.20.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MaldiAMRKit
-Version: 0.19.0
+Version: 0.20.0
 Summary: A comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes
 Author-email: Ettore Rocchi <ettore.rocchi3@unibo.it>
 License-Expression: MIT
@@ -52,6 +52,11 @@ Requires-Dist: hypothesis>=6.0.0; extra == "dev"
 Provides-Extra: batch
 Requires-Dist: umap-learn>=0.5; extra == "batch"
 Requires-Dist: combatlearn>=1.3; extra == "batch"
+Provides-Extra: formats
+Requires-Dist: pyteomics>=4.0; extra == "formats"
+Requires-Dist: lxml>=4.0; extra == "formats"
+Requires-Dist: psims>=1.0; extra == "formats"
+Requires-Dist: pynumpress>=0.1.5; python_version >= "3.11" and extra == "formats"
 Dynamic: license-file
 
 # MaldiAMRKit
@@ -108,6 +113,14 @@ pip install maldiamrkit[batch]
 
 Installs [`combatlearn`](https://github.com/EttoreRocchi/combatlearn) for ComBat-based batch effect correction and `umap-learn` for UMAP exploratory plots.
 
+### Optional: extended mzML/mzXML support
+
+```bash
+pip install maldiamrkit[formats]
+```
+
+`.mzML` and `.mzXML` files are read out of the box (zlib-compressed or uncompressed arrays). This extra installs [`pyteomics`](https://pyteomics.readthedocs.io/) with `lxml`, `psims`, and `pynumpress`, which additionally handle numpress-compressed arrays. `pynumpress` ships no wheels for Python 3.10, so numpress arrays need Python 3.11 or newer.
+
 ### Development Installation
 
 ```bash
@@ -160,9 +173,10 @@ pip install -e .[dev]
 - **Dataset Building & Loading**: `DatasetBuilder` and `DatasetLoader` with pluggable layout adapters (`FlatLayout`, `BrukerTreeLayout`, `DRIAMSLayout`, `MARISMaLayout`)
 - **Replicate Collapsing**: `DRIAMSLayout(collapse_replicates=True)` merges technical replicates (`_MALDI<N>`) to one row per isolate at load time via the active `duplicate_strategy`
 - **Bruker Format Support**: Read Bruker flexAnalysis binary data (fid/1r + acqus) natively via `read_spectrum()` on directories
+- **Open Formats**: Read `.mzML` and `.mzXML` files (optionally gzipped) via `read_spectrum()`, `MaldiSpectrum`, and `FlatLayout(spectrum_ext=".mzML")`; `pip install maldiamrkit[formats]` adds `pyteomics` for numpress-compressed arrays
 - **MIC Parsing**: `parse_mic_column()` for parsing MIC strings with qualifiers and European decimals
 - **Composable Filters**: `SpeciesFilter`, `DrugFilter`, `QualityFilter`, `MetadataFilter` combinable with `&`/`|`/`~` operators
-- **Spectrum Export**: Save spectra to CSV or TXT via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
+- **Spectrum Export**: Save spectra to CSV, TXT, or mzML via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
 
 ### Visualization & Tools
 - **Exploratory Plots**: PCA, t-SNE, and UMAP scatter plots colored by species, resistance phenotype, or any metadata column

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/README.md

@@ -52,6 +52,14 @@ pip install maldiamrkit[batch]
 
 Installs [`combatlearn`](https://github.com/EttoreRocchi/combatlearn) for ComBat-based batch effect correction and `umap-learn` for UMAP exploratory plots.
 
+### Optional: extended mzML/mzXML support
+
+```bash
+pip install maldiamrkit[formats]
+```
+
+`.mzML` and `.mzXML` files are read out of the box (zlib-compressed or uncompressed arrays). This extra installs [`pyteomics`](https://pyteomics.readthedocs.io/) with `lxml`, `psims`, and `pynumpress`, which additionally handle numpress-compressed arrays. `pynumpress` ships no wheels for Python 3.10, so numpress arrays need Python 3.11 or newer.
+
 ### Development Installation
 
 ```bash
@@ -104,9 +112,10 @@ pip install -e .[dev]
 - **Dataset Building & Loading**: `DatasetBuilder` and `DatasetLoader` with pluggable layout adapters (`FlatLayout`, `BrukerTreeLayout`, `DRIAMSLayout`, `MARISMaLayout`)
 - **Replicate Collapsing**: `DRIAMSLayout(collapse_replicates=True)` merges technical replicates (`_MALDI<N>`) to one row per isolate at load time via the active `duplicate_strategy`
 - **Bruker Format Support**: Read Bruker flexAnalysis binary data (fid/1r + acqus) natively via `read_spectrum()` on directories
+- **Open Formats**: Read `.mzML` and `.mzXML` files (optionally gzipped) via `read_spectrum()`, `MaldiSpectrum`, and `FlatLayout(spectrum_ext=".mzML")`; `pip install maldiamrkit[formats]` adds `pyteomics` for numpress-compressed arrays
 - **MIC Parsing**: `parse_mic_column()` for parsing MIC strings with qualifiers and European decimals
 - **Composable Filters**: `SpeciesFilter`, `DrugFilter`, `QualityFilter`, `MetadataFilter` combinable with `&`/`|`/`~` operators
-- **Spectrum Export**: Save spectra to CSV or TXT via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
+- **Spectrum Export**: Save spectra to CSV, TXT, or mzML via `MaldiSpectrum.save()` and `MaldiSet.save_spectra()`
 
 ### Visualization & Tools
 - **Exploratory Plots**: PCA, t-SNE, and UMAP scatter plots colored by species, resistance phenotype, or any metadata column

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/maldiamrkit/__init__.py

@@ -27,7 +27,7 @@ Examples
 from .dataset import MaldiSet
 from .spectrum import MaldiSpectrum
 
-__version__ = "0.19.0"
+__version__ = "0.20.0"
 __author__ = "Ettore Rocchi"
 
 __all__ = [

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/maldiamrkit/data/input_layouts.py

@@ -80,6 +80,10 @@ class FlatLayout(InputLayout):
         ``spectra_dir`` is itself flat but the years are known from another
         source. Takes precedence over the inferred subfolder year,
         but not over ``year_column``.
+    spectrum_ext : str, default=".txt"
+        File extension of the spectrum files.  Any format understood by
+        :func:`~maldiamrkit.io.read_spectrum` works, e.g. ``".mzML"`` or
+        ``".mzXML"`` for open-format exports.
     """
 
     def __init__(
@@ -90,30 +94,39 @@ class FlatLayout(InputLayout):
         id_column: str = "ID",
         year_column: str | None = None,
         year_overrides: dict[str, str] | None = None,
+        spectrum_ext: str = ".txt",
     ) -> None:
         self.spectra_dir = Path(spectra_dir)
         self.metadata_csv = Path(metadata_csv)
         self.id_column = id_column
         self.year_column = year_column
         self.year_overrides = year_overrides
+        self.spectrum_ext = (
+            spectrum_ext if spectrum_ext.startswith(".") else f".{spectrum_ext}"
+        )
         self._year_map: dict[str, str] | None = None
         self._folder_year_map: dict[str, str] = {}
 
     def discover_spectra(self) -> list[Path]:
-        """Find ``.txt`` files, whether flat or in (possibly nested) subfolders.
+        """Find spectrum files, whether flat or in (possibly nested) subfolders.
+
+        The extension is ``spectrum_ext`` (``.txt`` by default).
 
         Files are searched flat first, then one level down, then
         recursively. Whenever a spectrum sits under a four-digit-year
         folder, that year is recorded so it can serve as a fallback when
         no ``year_column`` is supplied (see :meth:`get_year`).
         """
-        files = sorted(self.spectra_dir.glob("*.txt"))
+        pattern = f"*{self.spectrum_ext}"
+        files = sorted(self.spectra_dir.glob(pattern))
         if not files:
-            files = sorted(self.spectra_dir.glob("*/*.txt"))
+            files = sorted(self.spectra_dir.glob(f"*/{pattern}"))
         if not files:
-            files = sorted(self.spectra_dir.rglob("*.txt"))
+            files = sorted(self.spectra_dir.rglob(pattern))
         if not files:
-            raise ValueError(f"No .txt spectrum files found in {self.spectra_dir}")
+            raise ValueError(
+                f"No {self.spectrum_ext} spectrum files found in {self.spectra_dir}"
+            )
 
         self._folder_year_map = {}
         for f in files:

{maldiamrkit-0.19.0 → maldiamrkit-0.20.0}/maldiamrkit/dataset.py

@@ -625,8 +625,9 @@ class MaldiSet:
             Which processing stage to save. One of ``"raw"``,
             ``"preprocessed"``, ``"binned"``.
         fmt : str, default="txt"
-            Output format. ``"csv"`` for comma-separated, ``"txt"`` for
-            tab-separated.
+            Output format, also used as file extension. ``"csv"`` for
+            comma-separated, ``"txt"`` for tab-separated, ``"mzML"`` for
+            mzML files.
 
         Raises
         ------