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Taxonomic Classes

Project description

pytaxa

pypi travis coverage

info

  • Minimum Python version: 3.5
  • pytaxa docs
  • Check out sister R package: taxa

Installation

Stable version

pip install pytaxa
pip3 install pytaxa

Dev version

sudo pip install git+git://github.com/sckott/pytaxa.git#egg=pytaxa

# OR

git clone git@github.com:sckott/pytaxa.git
cd pytaxa
make install

Usage

from pytaxa import constructors as cs
cs.taxon_name("Poa")

from pytaxa import Taxon
x = Taxon(None)
x.is_empty()

name = cs.taxon_name("Poa")
rank = cs.taxon_rank("genus", "ncbi")
db = cs.taxon_database("ncbi",
  "http://www.ncbi.nlm.nih.gov/taxonomy",
  "NCBI Taxonomy Database",
  "*")
id = cs.taxon_id(12345, db)
tx1 = Taxon(name, rank, id, "L.")
tx2 = Taxon(cs.taxon_name("Poaceae"),
  cs.taxon_rank("family", "ncbi"), cs.taxon_id(4479, db))
tx3 = Taxon(cs.taxon_name("Poa annua"),
  cs.taxon_rank("species", "ncbi"), cs.taxon_id(93036, db))
from pytaxa import Taxa
Taxa(tx1, tx2, tx3)

from pytaxa import Hierarchy
out = Hierarchy(tx1, tx2, tx)
out.taxa
out.ranklist
out.all_empty()
out.pop(ranks = "family")

Contributing

See CONTRIBUTING.md

Meta

Changelog

0.0.6 (2018-06-26)

  • First pypi release

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