Metadata-Version: 2.1
Name: pytrapment
Version: 1.0.1
Summary: pytrapment: create an entrapment database for proteomic mass spectrometry analysis
Home-page: UNKNOWN
Author: Sven Giese
Author-email: sven.giese@hpi.de
License: Apache License 2.0
Project-URL: Bug Tracker, https://github.com/gieses/pytrapment/issues
Project-URL: Source Code, https://github.com/gieses/pytrapment
Project-URL: Documentation, https://github.com/gieses/pytrapment
Project-URL: Homepage, https://github.com/gieses/pytrapment
Description: 
        [![GitHub](https://flat.badgen.net/github/license/gieses/pytrapment)](https://www.apache.org/licenses/LICENSE-2.0)
        [![Twitter](https://flat.badgen.net/twitter/follow/SvenHGiese?icon=twitter)](https://twitter.com/SvenHGiese)
        [![Python 3.8.3](https://img.shields.io/badge/python-3.8.3-blue.svg)](https://www.python.org/downloads/release/python-370/)
        
        A python package for creating entrapment databases.
        
        ---
        - [Overview](#overview)
        - [Installation](#Installation)
        ---
        
        ## overview
        
        pytrapment allows the convenient creation of entrapment databases for proteomic mass spectrometry analysis.
        Entrapment databases are build by sampling for each protein in the host fasta file an fitting
        entrapment protein.
        
        pytrapment performs the following steps to minimize the differences between the host and entrapment
        database.
        
        1. remove all entrapment proteins that share a peptide with the host (replace I with L amino acids)
        2. compute the amino acid composition for each protein in the host and entrapment database
        3. for each host protein find the nearest neighbor (Euclidean distance) in the composition space
        4. perform some quality control metrics on the peptides
        5. save the entrapment fasta file (host + entrapment proteins)   
        
        
        ## Installation
        pytrapment is available on pypi and can be installed via ```pip install pytrapment```
        
        ## Usage
        
        To use pytrapment, simply call the main program via a command line:
        
        ```
        pytrapment -i host.fasta -t trap.fasta -o entrapment_db
        ```
        
        Make sure to have the correct paths to the fasta files. The out dir will contain the entrapment
        fasta and two qc plots for peptide and protein features. The repository contains example files
        which can be used as follows:
        
        ```
        pytrapment -i sample_data/host.fasta -t sample_data/trap.fasta -o sample_data/
        ```
        
        The results (qc_plot.png and entrapment_data.fasta) can also be found in the sample_data folder.
        ## Contributors
        - Sven Giese
Keywords: Proteomics,machine learning,uniprot,fasta
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.8.0
Description-Content-Type: text/markdown
