Metadata-Version: 2.1
Name: taxtree
Version: 1.0.4
Summary: Python library for NCBI taxonomy database.
Home-page: https://github.com/bushenjie/taxtree
Author: bushenjie
Author-email: bushenjie@gmail.com
License: MIT
Description: 
        # TaxTree: Python library for NCBI taxonomy database
        
        Supported features:
        
        
        1. download data from NCBI automatically.
        2. use SQLite and SQLAlchemy to persist data.
        3. retrieve ancestor taxonomy in any rank.
        
        ## installation
        
        ```
        pip install taxtree
        ```
        
        ## usage
        
        ### initialize database
        
        Just run:
        
        ```
        taxtree
        ```
        
        1. All data were saved to `~/.taxtree`
        2. Downloaded `taxdmp.zip` path: `~/.taxtree/taxdmp.zip`
        3. Persistent data file path: `~/.taxtree/taxtree.db`
        
        ### search taxonomy
        
        ```python
        from taxtree import get_scoped_session, Tax
        
        with get_scoped_session() as session:
            tax = session.query(Tax).filter_by(tax_id='9606').first()
        ```
        
        
        ### get ancestor
        
        ```python
        from taxtree import get_scoped_session, Tax, KINGDOM, PHYLUM
        
        with get_scoped_session() as session:
            tax = session.query(Tax).filter_by(tax_id='9606').first()
            kingdom_tax = tax.get_ancestor(KINGDOM)
            phylum_tax = tax.get_ancestor(PHYLUM)
        ```
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
