{ "info": { "author": "Peter Kruczkiewicz", "author_email": "peter.kruczkiewicz@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: Apache Software License", "Natural Language :: English", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7" ], "description": "=================================================\nStandalone HTML Interactive Phylogenetic Tree Viz\n=================================================\n\n\n.. image:: https://img.shields.io/pypi/v/shiptv.svg\n :target: https://pypi.python.org/pypi/shiptv\n\n.. image:: https://img.shields.io/travis/peterk87/shiptv.svg\n :target: https://travis-ci.org/peterk87/shiptv\n\n.. image:: https://readthedocs.org/projects/shiptv/badge/?version=latest\n :target: https://shiptv.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n\n\nGenerate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas\n\n\n* Free software: Apache Software License 2.0\n* Documentation: https://shiptv.readthedocs.io.\n\n*See test shiptv HTML output here:*\n\n- `fmdv-5-shiptv.html`_\n\n\n**Phylogenetic tree of 5 FMDV genomes**\n\n.. image:: docs/images/fmdv5.png\n :alt: Phylogenetic tree of 5 FMDV genomes\n\n**Phylogenetic tree of IAV HA gene sequences**\n\n.. image:: docs/images/iav-ha-gene-tree-scrn.png\n :alt: Phylogenetic tree of IAV HA gene sequences\n\n\nFeatures\n--------\n\n* Interactively view your tree in the browser with metadata highlighted beside your tree using PhyloCanvas.\n* Automatically retrieve metadata from a GenBank file!\n* Visualize your own metadata! Provide a tab-delimited table as input with ``--user-sample-metadata /path/to/your-table.tsv``\n* Highlight branches with low support in the browser.\n* 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). \n\nUsage\n-----\n\nShow help\n\n.. code-block:: bash\n\n shiptv --help\n\n\nHelp output\n\n.. code-block:: \n\n Usage: shiptv [OPTIONS]\n\n Create HTML tree visualization with metadata.\n\n The metadata for reference genomes can be extracted from the specified\n Genbank file.\n\n Any leaf names that are present in the tree but not present in the Genbank\n file are assumed to be user samples and are flagged as such in the\n metadata table as \"user_sample\"=\"Yes\".\n\n Options:\n -r, --ref-genomes-genbank FILE Reference genome sequences Genbank file\n -n, --newick FILE Phylogenetic tree Newick file [required]\n -N, --output-newick PATH Output Newick file\n -o, --output-html PATH Output HTML tree path [required]\n -m, --output-metadata-table PATH\n Output metadata table path [required]\n --leaflist PATH Optional leaf names to select from\n phylogenetic tree for pruned tree\n visualization. One leaf name per line.\n --genbank-metadata-fields PATH Optional fields to extract from Genbank\n source metadata. One field per line.\n --user-sample-metadata PATH Optional tab-delimited metadata for user\n samples to join with metadata derived from\n reference genome sequences Genbank file.\n Sample IDs must be in the first column.\n --metadata-fields-in-order PATH\n Optional list of fields in order to output\n in metadata table and HTML tree\n visualization. One field per line.\n --dont-fix-metadata Do not automatically fix metadata (only on\n Genbank file metadata)\n -C, --collapse-support FLOAT Collapse internal branches below specified\n bootstrap support value (default -1 for no\n collapsing)\n --help Show this message and exit.\n\n\nWith 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`.\n\n.. code-block:: bash\n\n shiptv -r ref.gb -n tree.nwk -o tree.html -m metadata-table.tsv\n\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _`fmdv-5-shiptv.html`: docs/data/fmdv-5-shiptv.html\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: 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