Metadata-Version: 1.1
Name: shiptv
Version: 0.3.0
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.
        
        *See test shiptv HTML output here:*
        
        - `fmdv-5-shiptv.html`_
        
        
        **Phylogenetic tree of 5 FMDV genomes**
        
        .. image:: docs/images/fmdv5.png
                :alt: Phylogenetic tree of 5 FMDV genomes
        
        **Phylogenetic tree of IAV HA gene sequences**
        
        .. image:: docs/images/iav-ha-gene-tree-scrn.png
                :alt: Phylogenetic tree of IAV HA gene sequences
        
        
        Features
        --------
        
        * Interactively view your tree in the browser with metadata highlighted beside your tree using PhyloCanvas.
        * Automatically retrieve metadata from a GenBank file!
        * Visualize your own metadata! Provide a tab-delimited table as input with ``--user-sample-metadata /path/to/your-table.tsv``
        * Highlight branches with low support in the browser.
        * Collapse branches with low support (e.g. ``-C 95`` for IQ-TREE trees with UFBoot ``-bb 1000`` to collapse branches with less than 95% support). 
        
        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 can be 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 FILE  Reference genome sequences Genbank file
              -n, --newick FILE               Phylogenetic tree Newick file  [required]
              -N, --output-newick PATH        Output Newick file
              -o, --output-html PATH          Output HTML tree path  [required]
              -m, --output-metadata-table PATH
                                              Output metadata table path  [required]
              --leaflist PATH                 Optional leaf names to select from
                                              phylogenetic tree for pruned tree
                                              visualization. One leaf name per line.
              --genbank-metadata-fields PATH  Optional fields to extract from Genbank
                                              source metadata. One field per line.
              --user-sample-metadata PATH     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 PATH
                                              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 (only on
                                              Genbank file metadata)
              -C, --collapse-support FLOAT    Collapse internal branches below specified
                                              bootstrap support value (default -1 for no
                                              collapsing)
              --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.
        
        .. _`fmdv-5-shiptv.html`: docs/data/fmdv-5-shiptv.html
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.2.0 (2019-06-28)
        ------------------
        
        * Added low support branch highlighting in tree HTML file
        * Added option to collapse low support branches (`-C/--collapse-support`)
        * Added option to output modified Newick tree file (`-N/--output-newick`)
        * Fixed date/time parsing from Genbank files (#1)
        
        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
