Metadata-Version: 2.1
Name: spectrum_utils
Version: 0.1.0
Summary: Mass spectrometry utility functions
Home-page: https://github.com/bittremieux/spectrum_utils
Author: Wout Bittremieux
Author-email: wout.bittremieux@uantwerpen.be
License: Apache 2.0
Description: # spectrum_utils
        
        [![Build status](https://travis-ci.org/bittremieux/spectrum_utils.svg?master)](https://travis-ci.org/bittremieux/spectrum_utils)
        ![Python 3.6](https://img.shields.io/badge/python-3.6-brightgreen.svg)
        ![Python 3.7](https://img.shields.io/badge/python-3.7-brightgreen.svg)
        
        Simple MS/MS spectrum preprocessing and visualization in Python.
        
        ## Features
        
        - Spectrum (pre)processing
        	- Precursor & noise peak removal
        	- Intensity filtering
        	- Intensity scaling
        	- Fragment ion annotating (powered by [Pyteomics](https://pyteomics.readthedocs.io/))
        - Spectrum plotting
        	- Single spectrum with annotated ions
        	- Mirror plot of matching spectra
        
        ## Example
        
        ```
        import matplotlib.pyplot as plt
        
        from spectrum_utils import plot
        from spectrum_utils import spectrum
        
        
        # Initialize spectrum information first...
        
        spec = spectrum.MsmsSpectrum(identifier, precursor_mz, precursor_charge,
                                     mz, intensity, retention_time=retention_time,
                                     peptide=peptide)
        
        # Preprocess the MS/MS spectrum.
        fragment_tol_mass = 10
        fragment_tol_mode = 'ppm'
        spec = (spec.set_mz_range(min_mz=100, max_mz=1400)
                    .remove_precursor_peak(fragment_tol_mass, fragment_tol_mode)
                    .filter_intensity(min_intensity=0.05, max_num_peaks=150)
                    .scale_intensity(scaling='root')
                    .annotate_peaks(fragment_tol_mass, fragment_tol_mode,
                                    ion_types='aby'))
        
        # Plot the MS/MS spectrum.
        plot.spectrum(spec)
        
        plt.show()
        plt.close()
        ```
        (Condensed example. See [here](https://github.com/bittremieux/spectrum_utils/blob/master/notebooks/preprocess_and_plot.ipynb) for the full code to generate the figure below.)
        
        ![spectrum_utils](spectrum_utils.png)
        
        ## Installation
        
        `spectrum_utils` can be installed easily via pip:
        
        ```pip install spectrum_utils```
        
        <!--Or via conda:
        
        ```conda install spectrum_utils -c bioconda```-->
        
        ### Dependencies
        
        `spectrum_utils` has the following dependencies:
        
        - [Matplotlib](https://matplotlib.org/)
        - [Numba](http://numba.pydata.org/)
        - [NumPy](https://www.numpy.org/)
        - [Pyteomics](https://pyteomics.readthedocs.io/)
        
        Missing dependencies will be automatically installed when you install `spectrum_utils`.
        
        ## API documentation
        
        You can find the API documentation [here](https://spectrum-utils.readthedocs.io/).
        
        ## Contact
        
        For more information you can visit the [official code website](https://github.com/bittremieux/spectrum_utils/) or send an email to <wout.bittremieux@uantwerpen.be>.
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
