Metadata-Version: 1.1
Name: shiptv
Version: 0.1.0
Summary: Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas
Home-page: https://github.com/peterk87/shiptv
Author: Peter Kruczkiewicz
Author-email: peter.kruczkiewicz@gmail.com
License: Apache Software License 2.0
Description: =================================================
        Standalone HTML Interactive Phylogenetic Tree Viz
        =================================================
        
        
        .. image:: https://img.shields.io/pypi/v/shiptv.svg
                :target: https://pypi.python.org/pypi/shiptv
        
        .. image:: https://img.shields.io/travis/peterk87/shiptv.svg
                :target: https://travis-ci.org/peterk87/shiptv
        
        .. image:: https://readthedocs.org/projects/shiptv/badge/?version=latest
                :target: https://shiptv.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        
        Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas
        
        
        * Free software: Apache Software License 2.0
        * Documentation: https://shiptv.readthedocs.io.
        
        
        Features
        --------
        
        * TODO
        
        Usage
        -----
        
        Show help
        
        .. code-block:: bash
        
            shiptv --help
        
        
        Help output
        
        .. code-block:: 
        
            Usage: shiptv [OPTIONS]
        
              Create HTML tree visualization with metadata.
        
              The metadata for reference genomes is extracted from the specified Genbank
              file.
        
              Any leaf names that are present in the tree but not present in the Genbank
              file are assumed to be user samples and are flagged as such in the
              metadata table as "user_sample"="Yes".
        
            Options:
              -r, --ref-genomes-genbank TEXT  Reference genome sequences Genbank file
                                              [required]
              -n, --newick TEXT               Phylogenetic tree Newick file  [required]
              -o, --output-html TEXT          Output HTML tree path  [required]
              -m, --output-metadata-table TEXT
                                              Output metadata table path  [required]
              --leaflist TEXT                 Optional leaf names to select from
                                              phylogenetic tree for pruned tree
                                              visualization. One leaf name per line.
              --genbank-metadata-fields TEXT  Optional fields to extract from Genbank
                                              source metadata. One field per line.
              --user-sample-metadata TEXT     Optional tab-delimited metadata for user
                                              samples to join with metadata derived from
                                              reference genome sequences Genbank file.
                                              Sample IDs must be in the first column.
              --metadata-fields-in-order TEXT
                                              Optional list of fields in order to output
                                              in metadata table and HTML tree
                                              visualization. One field per line.
              --dont-fix-metadata             Do not automatically fix metadata
              --help                          Show this message and exit.
        
        
        With a reference sequence Genbank file `ref.gb`, a Newick format phylogenetic tree `tree.nwk`, output a `tree.html` standalone HTML interactive phylogenetic tree visualization and a `metadata-table.tsv` tab-delimited table of metadata from `ref.gb`.
        
        .. code-block:: bash
        
            shiptv -r ref.gb -n tree.nwk -o tree.html -m metadata-table.tsv
        
        
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.1.0 (2019-05-10)
        ------------------
        
        * First release on PyPI.
        
Keywords: shiptv
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
