| Name | flattaxdb JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | |
| Summary | Yet another Python library to work with taxonomy databases |
| upload_time | 2023-06-30 13:49:42 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.9 |
| license | The MIT License (MIT) Copyright (c) 2023 Brandon Seah Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
taxonomy
ncbi
gbif
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
Parse and query different taxonomic databases
=============================================
Aims
----
* Work with taxonomic databases from data dump flatfiles.
* Load them directly into memory for queries and other operations.
* Use same internal data structures and methods for different source DBs.
* Report output as far as possible with DwC terms.
Such functionality is available with the R package
[`taxadb`](https://github.com/ropensci/taxadb), but we wish to work in Python
with few dependencies as possible.
Databases supported
-------------------
* NCBI Taxonomy (names.dmp and nodes.dmp file from taxdump)
* Tested with version [2022-12-01](https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-12-01.zip)
* GBIF Backbone Taxonomy (Taxon.tsv file from backbone dump)
* Tested with version [2021-11-26](https://hosted-datasets.gbif.org/datasets/backbone/2021-11-26/backbone.zip)
Raw data
{
"_id": null,
"home_page": "",
"name": "flattaxdb",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": "",
"keywords": "taxonomy,NCBI,GBIF",
"author": "",
"author_email": "Brandon Seah <brandon.seah@thuenen.de>",
"download_url": "https://files.pythonhosted.org/packages/41/31/5792713ef0bbc8cb12c894f6f5ea2d6670544ae5f4fba3fd5564d6226860/flattaxdb-0.1.0.tar.gz",
"platform": null,
"description": "Parse and query different taxonomic databases\n=============================================\n\nAims\n----\n* Work with taxonomic databases from data dump flatfiles.\n* Load them directly into memory for queries and other operations.\n* Use same internal data structures and methods for different source DBs.\n* Report output as far as possible with DwC terms.\n\nSuch functionality is available with the R package\n[`taxadb`](https://github.com/ropensci/taxadb), but we wish to work in Python\nwith few dependencies as possible.\n\n\nDatabases supported\n-------------------\n* NCBI Taxonomy (names.dmp and nodes.dmp file from taxdump)\n * Tested with version [2022-12-01](https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-12-01.zip)\n* GBIF Backbone Taxonomy (Taxon.tsv file from backbone dump)\n * Tested with version [2021-11-26](https://hosted-datasets.gbif.org/datasets/backbone/2021-11-26/backbone.zip)\n",
"bugtrack_url": null,
"license": " The MIT License (MIT) Copyright (c) 2023 Brandon Seah Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ",
"summary": "Yet another Python library to work with taxonomy databases",
"version": "0.1.0",
"project_urls": null,
"split_keywords": [
"taxonomy",
"ncbi",
"gbif"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "051e7e6466e39d4bc22d766c42c1b7aeefab76c474a3077eda6adf1ba93d71a5",
"md5": "e1ee31b45659c31a36fb5e835c1ff0d0",
"sha256": "df892947b9255d6d05eb27a742a6462732561c9c8d7aabad2e8e19b3cd674938"
},
"downloads": -1,
"filename": "flattaxdb-0.1.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "e1ee31b45659c31a36fb5e835c1ff0d0",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.9",
"size": 7531,
"upload_time": "2023-06-30T13:49:40",
"upload_time_iso_8601": "2023-06-30T13:49:40.197549Z",
"url": "https://files.pythonhosted.org/packages/05/1e/7e6466e39d4bc22d766c42c1b7aeefab76c474a3077eda6adf1ba93d71a5/flattaxdb-0.1.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "41315792713ef0bbc8cb12c894f6f5ea2d6670544ae5f4fba3fd5564d6226860",
"md5": "f9c960c92f2b4cfc9ee900d7aa525281",
"sha256": "e7e1a7adb2875d1b66944ac8f3c72826d478342157378ff63928b3efb102d413"
},
"downloads": -1,
"filename": "flattaxdb-0.1.0.tar.gz",
"has_sig": false,
"md5_digest": "f9c960c92f2b4cfc9ee900d7aa525281",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9",
"size": 7444,
"upload_time": "2023-06-30T13:49:42",
"upload_time_iso_8601": "2023-06-30T13:49:42.638306Z",
"url": "https://files.pythonhosted.org/packages/41/31/5792713ef0bbc8cb12c894f6f5ea2d6670544ae5f4fba3fd5564d6226860/flattaxdb-0.1.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-06-30 13:49:42",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "flattaxdb"
}
