Metadata-Version: 2.1
Name: pynomer
Version: 0.1.3
Summary: A python wrapper for nomer
Home-page: https://github.com/nleguillarme/pynomer
Author: Nicolas Le Guillarme
Author-email: nicolas.leguillarme@univ-grenoble-alpes.fr
License: MIT
Description: pynomer
        =======
        
        .. image:: https://img.shields.io/pypi/v/pynomer.svg
            :target: https://pypi.python.org/pypi/pynomer
            :alt: Latest PyPI version
        
        `pynomer <https://github.com/nleguillarme/pynomer>`_ is a simple python wrapper for `nomer <https://github.com/globalbioticinteractions/nomer>`_.
        Nomer is a stand-alone java application which maps identifiers and names to taxonomic names and ontological terms.
        
        Installation
        ------------
        
        ::
        
          $ pip install pynomer
        
        Usage
        -----
        
        As a command-line tool
        **********************
        
        ::
        
          pynomer --help
          Usage: pynomer [OPTIONS] COMMAND [ARGS]...
        
            Options:
              --help  Show this message and exit.
        
            Commands:
              append              Append term match to row using id and name columns...
              clean               Cleans term matcher cache.
              input-schema        Show input schema in JSON.
              matchers            Lists supported matcher and (optionally) their...
              output-schema       Show output schema.
              properties          Lists configuration properties.
              replace             Replace exact term matches in row.
              validate-term       Validate terms.
              validate-term-link  Validate term links.
              version             Show Version.
              
        As a python module
        **********************
        
        ::
        
            >>> from pynomer import *
            >>> version()
            '0.1.18'
        
        With Docker
        **********************
        
        Build image from source:
        ::
        
            git clone https://github.com/nleguillarme/pynomer.git
            cd pynomer
            docker build -t pynomer:latest .
        
        Run commands in the container:
        ::
        
            docker run -v `pwd`/.nomer:/.nomer pynomer:latest pynomer append "\tHomo sapiens" -e -o json
            
        |:warning:| When running pynomer append and replace commands in Docker, you have to use the -e option !
        
        License
        -------
        
        License: MIT
        
        Authors
        -------
        
        `pynomer` was written by `nleguillarme <nicolas.leguillarme@univ-grenoble-alpes.fr>`_.
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
