Metadata-Version: 2.1
Name: minedatabase
Version: 1.0.0
Summary: Metabolic In silico Network Expansions
Home-page: https://github.com/tyo-nu/MINE-Database
Author: Jonathan Strutz
Author-email: jonstrutz11@gmail.com
License: MIT
Description: # MINE Databases
        [![Build Status](https://travis-ci.org/JamesJeffryes/MINE-Database.svg?branch=master)](https://travis-ci.org/JamesJeffryes/MINE-Database)
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        [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
        
        This repository contains code for the generation (though Pickaxe), 
        storage and querying of MINE databases. For generalinformation on MINE 
        Databases, please consult [JJeffryes et al. 2015](http://jcheminf.springeropen.com/articles/10.1186/s13321-015-0087-1)
        APIs can found in [the API Repository](https://github.com/tyo-nu/MINE-API)
        
        ## Repository Structure
        This repository primarily consists of the minedatabases python module 
        and it's 5 submodules:
        - compound_io: Contains functions to load and export chemical structures 
        from MINE databases. Has command-line interface.
        - databases: Contains functions which impose a schema on the underlying 
        Mongo databases which store MINE data.
        - pickaxe: Allows for the application of reaction rules to compound sets 
        and the annotation of the resulting compounds an reactions. Has command-line interface.
        - queries: Contains logic for text and chemical structure queries of the 
        MINE database.
        - utils: Various utility functions such as hashing & type conversions
        
        ### Compound_io command-line usage
        compound_io may be called independently to import or export chemical 
        strictures in MINE database format. These may be helpful for sharing 
        predictions or maintaining current external databases for cross-referencing.
        The call format is `python compound_io.py import-<format> <input path> 
        <database>` for imports and `python compound_io.py export-<format> 
        <database> <outfile path> <optionally: maximum compounds per file>` for exports.
        Valid formats are:
        - smi: SMILES line-code
        - mol: MDL molecule files (outputs individual files in specified directory)
        - sdf: Structured Data File (concatenated mol files)
        - tsv: FOR EXPORT ONLY, a tab separated file compatible with ModelSEED
        
        ### Pickaxe command-line usage
        Pickaxe.py can be called independently to generate predictions with or 
        without database storage. To list all options call `python pickaxe.py -h`. 
        To predict all chemical damage reactions for one generation on compounds in the iAF1260 
        model one would call `python pickaxe.py -C ./data/ChemicalDamageCoreactants.tsv -r 
        ./data/ChemicalDamageRxnRules.tsv -g 1 -c ./data/iAF1260.tsv`
        
        ### Testing
        `pytest` to run all tests. Ensure that pytest is installed.
        To add coverage, run:
        `pytest --cov-report term --cov-report xml:tests/cov.xml --cov=minedatabase minedatabase/tests/`
        Ensure that coverage and pytest-cov are both installed.
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
