shiptv 0.1.0

Generate a standalone HTML file with an interactive phylogenetic tree using PhyloCanvas

Standalone HTML Interactive Phylogenetic Tree Viz

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

shiptv --help

Help output

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.

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.

History

0.1.0 (2019-05-10)

• First release on PyPI.