# gtdb-itol-decorate
Creates iTOL files for tree decoration, given a set of GTDB genomes.
## Installation
```bash
pip install gtdb-itol-decorate
```
## Usage
This program requires a taxonomy file (available from the [GTDB website](https://data.gtdb.ecogenomic.org/releases/latest/)),
e.g. `bac120_taxonomy.tsv`, or `ar53_taxonomy.tsv`.
```bash
gtdb_itol_decorate /path/to/tree.tree /path/to/taxonomy.tsv /path/to/output
```
## Output
The program will output the following files.
Note: Typical use will be:
1. Upload `[name_of_input_tree].tree_stripped`
2. Drag the following files into the tree: `itol_dataset_strip_phylum.txt`, `itol_labels.txt`, `itol_popup.txt`, `itol_tree_colours.txt`
3. Use the `itol_collapse_[rank].txt` files to manipulate the view of the tree as desired.
### [name_of_input_tree].tree_stripped
This is the tree that you should upload to iTOL. It has been stripped of all
internal labels to match the iTOL tree format.
### itol_collapse_[rank].txt
When this file is dropped into the iTOL tree, it will [collapse](https://itol.embl.de/help.cgi#coll)
all nodes at this rank.
### itol_dataset_strip_phylum.txt
This file will create a new [colour strip](https://itol.embl.de/help.cgi#strip)
for each phylum.
### itol_labels.txt
This will add taxon [labels](https://itol.embl.de/help.cgi#textlabels)
to the tree for both the internal and leaf nodes.
Note: To enable internal labels:
* Open the "Control panel"
* Select the "Advanced" tab.
* Under "Branch metadata display", make sure "Node IDs" is set to "Display".
### itol_popup.txt
This creates a [popup](https://itol.embl.de/help.cgi#popup) window when the
mouse is hovered over each leaf node. It will display the genome id, and full
taxonomy string.
### itol_tree_colours.txt
Creates a [colour range](https://itol.embl.de/help.cgi#colors) for each taxon,
based on the phylum colour. It will increase in brightness from phylum to species.
Note: This can be changed by altering the "Coloured ranges" popup that will
appear after adding this file. In the "Cover" option, "Clade" view is recommended.
Raw data
{
"_id": null,
"home_page": "https://github.com/Ecogenomics/gtdb-itol-decorate",
"name": "gtdb-itol-decorate",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": null,
"author": "Aaron Mussig",
"author_email": "aaronmussig@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/1f/af/e3b17b8388554287d3b2947f9eda4fd4b9c10af90d9f58057c320487b66b/gtdb_itol_decorate-1.1.1.tar.gz",
"platform": null,
"description": "# gtdb-itol-decorate\n\nCreates iTOL files for tree decoration, given a set of GTDB genomes.\n\n## Installation\n\n```bash\npip install gtdb-itol-decorate\n```\n\n## Usage\n\nThis program requires a taxonomy file (available from the [GTDB website](https://data.gtdb.ecogenomic.org/releases/latest/)), \ne.g. `bac120_taxonomy.tsv`, or `ar53_taxonomy.tsv`.\n\n```bash\ngtdb_itol_decorate /path/to/tree.tree /path/to/taxonomy.tsv /path/to/output\n```\n\n## Output\n\n\n\n\nThe program will output the following files.\n\nNote: Typical use will be:\n\n1. Upload `[name_of_input_tree].tree_stripped`\n2. Drag the following files into the tree: `itol_dataset_strip_phylum.txt`, `itol_labels.txt`, `itol_popup.txt`, `itol_tree_colours.txt`\n3. Use the `itol_collapse_[rank].txt` files to manipulate the view of the tree as desired.\n\n\n### [name_of_input_tree].tree_stripped\n\nThis is the tree that you should upload to iTOL. It has been stripped of all\ninternal labels to match the iTOL tree format.\n\n### itol_collapse_[rank].txt\n\nWhen this file is dropped into the iTOL tree, it will [collapse](https://itol.embl.de/help.cgi#coll)\nall nodes at this rank.\n\n### itol_dataset_strip_phylum.txt\n\nThis file will create a new [colour strip](https://itol.embl.de/help.cgi#strip) \nfor each phylum.\n\n\n\n### itol_labels.txt\n\nThis will add taxon [labels](https://itol.embl.de/help.cgi#textlabels) \nto the tree for both the internal and leaf nodes.\n\nNote: To enable internal labels:\n\n* Open the \"Control panel\"\n* Select the \"Advanced\" tab.\n* Under \"Branch metadata display\", make sure \"Node IDs\" is set to \"Display\".\n\n\n\n### itol_popup.txt\n\nThis creates a [popup](https://itol.embl.de/help.cgi#popup) window when the \nmouse is hovered over each leaf node. It will display the genome id, and full \ntaxonomy string.\n\n### itol_tree_colours.txt\n\nCreates a [colour range](https://itol.embl.de/help.cgi#colors) for each taxon, \nbased on the phylum colour. It will increase in brightness from phylum to species.\n\nNote: This can be changed by altering the \"Coloured ranges\" popup that will\nappear after adding this file. In the \"Cover\" option, \"Clade\" view is recommended.\n\n\n",
"bugtrack_url": null,
"license": "GPL-3.0",
"summary": "Creates iTOL files for tree decoration, given a set of GTDB genomes.",
"version": "1.1.1",
"project_urls": {
"Bug Tracker": "https://github.com/Ecogenomics/gtdb-itol-decorate",
"Documentation": "https://github.com/Ecogenomics/gtdb-itol-decorate",
"Homepage": "https://github.com/Ecogenomics/gtdb-itol-decorate",
"Source Code": "https://github.com/Ecogenomics/gtdb-itol-decorate"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "e91cd7f949d23b72655d8bdaa129d41eb2354998e7e2aec777969c92858e42d4",
"md5": "c4cb35901c35b408be60b54618d10645",
"sha256": "cd439eb33d91870ae2ace12854f4b898f6d7ca84a167803bc3451e292c55ae40"
},
"downloads": -1,
"filename": "gtdb_itol_decorate-1.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c4cb35901c35b408be60b54618d10645",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 22413,
"upload_time": "2025-01-17T00:36:24",
"upload_time_iso_8601": "2025-01-17T00:36:24.227525Z",
"url": "https://files.pythonhosted.org/packages/e9/1c/d7f949d23b72655d8bdaa129d41eb2354998e7e2aec777969c92858e42d4/gtdb_itol_decorate-1.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "1fafe3b17b8388554287d3b2947f9eda4fd4b9c10af90d9f58057c320487b66b",
"md5": "74cb1c3801baf8d1c9cb8f52e7754f41",
"sha256": "0dfbe79e18e12ab746a3b87689ba24740bcf18d2197b31ab3f8af8e5a9dece9f"
},
"downloads": -1,
"filename": "gtdb_itol_decorate-1.1.1.tar.gz",
"has_sig": false,
"md5_digest": "74cb1c3801baf8d1c9cb8f52e7754f41",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 21485,
"upload_time": "2025-01-17T00:36:25",
"upload_time_iso_8601": "2025-01-17T00:36:25.416113Z",
"url": "https://files.pythonhosted.org/packages/1f/af/e3b17b8388554287d3b2947f9eda4fd4b9c10af90d9f58057c320487b66b/gtdb_itol_decorate-1.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-01-17 00:36:25",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "Ecogenomics",
"github_project": "gtdb-itol-decorate",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "gtdb-itol-decorate"
}
JSON
