Merge pull request #379 from pymzml/feature/chromatogram_access

Addition of features to handle chromatograms

Author: StSchulze

docs/source/pymzml_spec.rst

@@ -30,8 +30,8 @@ Chromatogram
     :exclude-members: __repr__, __str__
 
 
-MS_Spectrum
+MsData
 -----------
 
-.. autoclass:: pymzml.spec.MS_Spectrum
+.. autoclass:: pymzml.msdata.MsData
     :members:

example_scripts/access_spectra_and_chromatograms.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import sys
+import pymzml
+
+
+def main(mzml_file):
+    """
+    Example script demonstrating how to access both spectra and chromatograms
+    using pymzML.
+
+    Usage:
+        ./access_spectra_and_chromatograms.py <path_to_mzml_file>
+    """
+    print("Initializing Reader...")
+    # Initialize with skip_chromatogram=False to include chromatograms during iteration
+    run = pymzml.run.Reader(mzml_file, skip_chromatogram=False)
+    
+    # Access the first spectrum using indexing (traditional way)
+    print("\nAccessing first spectrum using indexing (run[0]):")
+    try:
+        spectrum = run[0]
+        print(f"Spectrum ID: {spectrum.ID}")
+        print(f"MS Level: {spectrum.ms_level}")
+        print(f"Retention Time: {spectrum.scan_time_in_minutes()} minutes")
+        print(f"Number of peaks: {len(spectrum.peaks('raw'))}")
+    except Exception as e:
+        print(f"Error accessing spectrum: {e}")
+    
+    # Access the first spectrum using the new get_spectrum method
+    print("\nAccessing first spectrum using get_spectrum(0):")
+    try:
+        spectrum = run.get_spectrum(0)
+        print(f"Spectrum ID: {spectrum.ID}")
+        print(f"MS Level: {spectrum.ms_level}")
+        print(f"Retention Time: {spectrum.scan_time_in_minutes()} minutes")
+        print(f"Number of peaks: {len(spectrum.peaks('raw'))}")
+    except Exception as e:
+        print(f"Error accessing spectrum: {e}")
+    
+    # Access the TIC chromatogram using string identifier
+    print("\nAccessing TIC chromatogram using run['TIC']:")
+    try:
+        chromatogram = run["TIC"]
+        print(f"Chromatogram ID: {chromatogram.ID}")
+        print(f"Number of data points: {len(chromatogram.peaks())}")
+        
+        # Print the first few data points
+        print("\nFirst 5 data points (time, intensity):")
+        for i, (time, intensity) in enumerate(chromatogram.peaks()):
+            if i >= 5:
+                break
+            print(f"  {time:.4f}, {intensity:.2f}")
+    except Exception as e:
+        print(f"Error accessing chromatogram: {e}")
+    
+    # Access the first chromatogram using the new get_chromatogram method
+    print("\nAccessing first chromatogram using get_chromatogram(0):")
+    try:
+        chromatogram = run.get_chromatogram(0)
+        print(f"Chromatogram ID: {chromatogram.ID}")
+        print(f"Number of data points: {len(chromatogram.peaks())}")
+        
+        # Print the first few data points
+        print("\nFirst 5 data points (time, intensity):")
+        for i, (time, intensity) in enumerate(chromatogram.peaks()):
+            if i >= 5:
+                break
+            print(f"  {time:.4f}, {intensity:.2f}")
+    except Exception as e:
+        print(f"Error accessing chromatogram: {e}")
+    
+    # Demonstrate iterating through all items (spectra and chromatograms)
+    print("\nIterating through first few items (spectra and chromatograms):")
+    count = 0
+    for item in run:
+        if count >= 5:
+            break
+        if isinstance(item, pymzml.spec.Spectrum):
+            print(f"  Spectrum {item.ID}, MS level {item.ms_level}, RT {item.scan_time_in_minutes():.2f} min")
+        elif hasattr(item, 'time') and hasattr(item, 'i'):
+            print(f"  Chromatogram {item.ID}, {len(item.peaks())} data points")
+        count += 1
+    
+    print("\nDone!")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print(main.__doc__)
+        print("Please provide a path to an mzML file.")
+        sys.exit(1)
+    
+    mzml_file = sys.argv[1]
+    if not os.path.exists(mzml_file):
+        print(f"Error: File '{mzml_file}' not found.")
+        sys.exit(1)
+    
+    main(mzml_file)

pymzml/__init__.py

@@ -24,7 +24,7 @@
     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
     SOFTWARE.
 """
-__all__ = ["run", "spec", "obo", "minimum", "plot", "file_classes"]
+__all__ = ["run", "spec", "chromatogram", "obo", "minimum", "plot", "file_classes"]
 
 import sys
 
@@ -39,7 +39,9 @@
 # Imports of individual modules
 import pymzml.run
 import pymzml.spec
+import pymzml.chromatogram
 from pymzml.spec import MSDecoder
+from pymzml.chromatogram import Chromatogram
 import pymzml.obo
 import pymzml.plot
 import pymzml.utils