shiptv 0.2.0

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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.

使用参考序列genbank文件ref.gb，newick格式的系统发生树tree.nwk，输出一个tree.html独立的html交互式系统发生树可视化和一个元数据表.tsvtab分隔的元数据表。

shiptv -r ref.gb -n tree.nwk -o tree.html -m metadata-table.tsv

学分

这个包是用Cookiecutter和audreyr/cookiecutter-pypackage项目模板创建的。