Metadata-Version: 2.1
Name: mzmlripper
Version: 1.1.1
Summary: Extractor for MS1 and MS2 data from mzML file format
Home-page: https://github.com/croningp/mzmlripper
Author: Graham Keenan
Author-email: graham.keenan@glasgow.ac.uk
License: UNKNOWN
Description: # MzML Ripper
        
        This package parses MzML files and extracts data into JSON format for easier processing.
        
        
        Extracts the following information:
        
        * MS1 Information
        * MS2 Information
        * MS3 Information
        * MS4 Information
        
        
        * For each spectrum in MS1/2/3/4:
            * Masses and Intensities
            * Parent of that spectrum
            * Retention time of that spectrum
            * List of masses
        
        ---
        
        ## Installation
        
        Mzmlripper is available through Pip (Python Package Index):
        ```
        pip install mzmlripper --user
        ```
        
        Source code will be made available in due course.
        
        ### Dependencies
        If you want to use the (optional) SPectraL hASHing functions (see https://splash.fiehnlab.ucdavis.edu/ for more details), 
        you may want to install pySPLASH with the following commands:
        ```
        git clone git://github.com/berlinguyinca/spectra-hash.git
        cd spectra-hash/python
        python setup.py install
        
        ```
        
        ---
        
        ## Usage
        
        Import the extractor and give it a file/directory and an output directory for the JSON files
        
        ```python
        # Import module
        import mzmlripper.extractor as ripper
        
        # Process an mzML file
        ripper_data = ripper.process_mzml_file(mzml_filename, target_directory)
        
        # Using the pySPLASH functions
        import mzmlripper.splash_helpers as spl
        
        # Add splash to each ripper function
        splashed_ripper_data = spl.splash_ripper_dict(ripper_data)
        
        ```
        ---
        
        ## Output
        The file output is in the following format:
        
        ```json
        {
            "ms1": {
                "sppectrum_1": {
                    "95.3423": 160,
                    "96.8473": 322,
                    "110.8476": 640253,
                    ...
                    "parent": "",
                    "retention_time": "0.9685",
                    "mass_list": [
                        95.3423,
                        96.8473,
                        110.8476
                        ...
                    ]
                },
                "spectrum_2": {
                    ...
                },
                ...
            },
            "ms2": {
                "spectrum_1": {
                    "101.2356": 4552,
                    "102.5398": 12369,
                    "102.9856": 845,
                    ...
                    "parent": "235.6523",
                    "retention_time": "1.1203",
                    "mass_list": [
                        101.2356,
                        102.5398,
                        102.9856,
                        ...
                    ]
                },
                "spectrum_2": {
                    ...
                },
                ...
            },
            "ms3": {
                "spectrum_1": {
                    "67.3434": 142,
                    "69.8364": 1325,
                    "72.9746": 3320,
                    ...
                    "parent": "102.2365",
                    "retention_time": "1.0253",
                    "mass_list": [
                        67.3434,
                        69.8364,
                        72.9746,
                        ...
                    ]
                },
                "spectrum_2": {
                    ...
                },
                ...
            },
            "ms4": {
                "spectrum_1": {
                    "45.2036": 1234,
                    "46.3210": 8853,
                    "49.3205": 12342,
                    ...
                    "parent": "115.3256",
                    "retention_time": "2.0365",
                    "mass_list": [
                        45.2036,
                        46.3120,
                        49.3205,
                        ...
                    ]
                },
                "spectrum_2": {
                    ...
                },
                ...
            }
        }
        ```
        ---
        
        ## Authors
        
        All software was written as part of the [Cronin Lab 2019](http://www.chem.gla.ac.uk/cronin/)
        
        * [Graham Keenan](mailto:Graham.Keenan@glasgow.ac.uk)
        * [Dr. David Doran](mailto:d.doran.1@research.gla.ac.uk)
        * [Dr. Cole Mathis](mailto:Cole.Mathis@glasgow.ac.uk)
        
        ---
        
        ## Contributions
        
        * [Dr. Emma Carrick](mailto:Emma.Carrick@glasgow.ac.uk)
        
        
        ---
        
        ## License
        
        [![MIT](https://upload.wikimedia.org/wikipedia/commons/thumb/0/0c/MIT_logo.svg/220px-MIT_logo.svg.png)](https://opensource.org/licenses/MIT)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
