taxOrder

Package:

from taxOrder.taxOrder import order_taxa

taxorder = order_taxa(tree, 'Homo_sapiens', format=1, idmap='')

Command line implementation:

usage: taxOrder [-h] -t <path> -r str [--outfile [str]] [--format [str]] [--idmap [<path>]]

Returns list of species in a phylogenetic tree ordered by increasing taxonomic distance to a reference species


  -h, --help            show this help message and exit

  -t <path>, --tree <path>
                        Path to tree in Newick format

  -r , --reference str
                        Reference species

optional arguments:

  --outfile [str]       Save output to file

  --format [str]        Tree format as specified at: https://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees (Default: 1)

  --idmap [<path>]      TaxOrder can map species names to taxids accepted by PhyloProfile if supplied with a tab-seperated file like: taxid name

Metadata

Release files for taxOrder 0.2.7

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for taxOrder 0.2.7
File	Size	Uploaded
taxOrder-0.2.7.tar.gz	15.3 kB	Jul 7, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for taxOrder 0.2.7
File	Interpreter	ABI	Platform	Reset
taxOrder-0.2.7-py3-none-any.whl 16.1 kB Jul 7, 2023	Python 3	none	any	Details

Total release size: 31.4 kB

Release files / taxOrder-0.2.7.tar.gz

Download URL	taxOrder-0.2.7.tar.gz
Size	15.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`d72b7178ee5529a8f45cfe209f4628359505d0ac377299dd4c7bcfc2525b1afd`
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Uploaded via	`twine/4.0.2 CPython/3.11.0`

Release files / taxOrder-0.2.7-py3-none-any.whl

Download URL	taxOrder-0.2.7-py3-none-any.whl
Size	16.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`c87789d86b1bae4b665463b52f424cf1d43b278ab99e1b110dca0c0fc17c260b`
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Upload date	Jul 7, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.11.0`