pytaxize 0.7.0

Taxonomic toolbelt for Python

pytaxize

This is a port of the R package taxize. There is a lot going on in the R version of this library, so it will take a while to get all the same functionality over here.

Why? A significant advantage of a Python version of taxize will be for those that are pythonistas at heart. Also, you could use pytaxize in a web app, whereas you could with taxize (e.g., in a Shiny app), but it wouldn’t scale, be very fast, etc.

python 2/3

pytaxize is only developed in and tested with Python 3

Installation

Stable from pypi

pip install pytaxize

Development version

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

Taxonomic Ids

I’ve started working on a class interface for taxonomic IDs, which will have a bunch of extension methods to do various things with taxon ids. What’s available right now is just getting COL ids.

from pytaxize import Ids
res = Ids('Poa annua')
res.ncbi()
res.ids

{'Poa annua': [{'id': '93036',
   'name': 'Poa annua',
   'rank': 'species',
   'uri': 'https://www.ncbi.nlm.nih.gov/taxonomy/93036'}]}

Vascan search

import pytaxize
pytaxize.vascan_search(q = ["Helianthus annuus"])

{u'apiVersion': u'0.1',
 u'results': [{u'matches': [{u'canonicalName': u'Helianthus annuus',
     u'distribution': [{u'establishmentMeans': u'introduced',
       u'locality': u'NS',
       u'locationID': u'ISO 3166-2:CA-NS',
       u'occurrenceStatus': u'introduced'},
      {u'establishmentMeans': u'',
       u'locality': u'PE',
       u'locationID': u'ISO 3166-2:CA-PE',
       u'occurrenceStatus': u'excluded'},
      {u'establishmentMeans': u'',
       u'locality': u'NT',
       u'locationID': u'ISO 3166-2:CA-NT',
       u'occurrenceStatus': u'doubtful'},
      {u'establishmentMeans': u'introduced',

Scrape taxonomic names

out = pytaxize.scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf')
out['data'][0:3]

[{'verbatim': '(Hemiptera:',
  'scientificName': 'Hemiptera',
  'offsetStart': 222,
  'offsetEnd': 233},
 {'verbatim': 'Sternorrhyncha:',
  'scientificName': 'Sternorrhyncha',
  'offsetStart': 234,
  'offsetEnd': 249},
 {'verbatim': 'Coccoidea:',
  'scientificName': 'Coccoidea',
  'offsetStart': 250,
  'offsetEnd': 260}]

ITIS low level functions

from pytaxize import itis
itis.accepted_names(504239)

{'acceptedName': 'Dasiphora fruticosa',
   'acceptedTsn': '836659',
   'author': '(L.) Rydb.'}

itis.comment_detail(tsn=180543)

[{'commentDetail': 'Status: CITES - Appendix I as U. arctos (Mexico, Bhutan, China, and Mongolia populations) and U. a. isabellinus; otherwise Appendix II. U. S. ESA - Endangered as U. arctos pruinosus, as U. arctos in Mexico, and as U. a. arctos in Italy. Threatened as U. a. ho...',
  'commentId': '18556',
  'commentTimeStamp': '2007-08-20 15:06:38.0',
  'commentator': 'Wilson & Reeder, eds. (2005)',
  'updateDate': '2014-02-03'},
 {'commentDetail': "Comments: Reviewed by Erdbrink (1953), Couturier (1954), Rausch (1963a), Kurtén (1973), Hall (1984) and Pasitschniak-Arts (1993). Ognev (1931) and Allen (1938) recognized U. pruinosus as distinct; not followed by Ellerman and Morrison-Scott (1951), Gao (1987), and Stroganov (1962). Lönnberg (1923b) believed that differences between pruinosus and arctos warranted subgeneric distinction as (Mylarctos) pruinosus; however, this was not supported by Pocock's (1932b) thorough revision. Synonyms allocated a...",
  'commentId': '18557',
  'commentTimeStamp': '2007-08-20 15:06:38.0',
  'commentator': 'Wilson & Reeder, eds. (2005)',
  'updateDate': '2014-02-03'}]

itis.hierarchy_up(tsn = 36485)

{'author': 'Raf.',
 'parentName': 'Asteraceae',
 'parentTsn': '35420',
 'rankName': 'Genus',
 'taxonName': 'Agoseris',
 'tsn': '36485'}

Catalogue of Life

from pytaxize import col
x = col.children(name=["Apis"])
x[0][0:3]

[{'id': '7a4a38c5095963949d6d6ec917d471de',
  'name': 'Apis andreniformis',
  'rank': 'Species'},
 {'id': '39610a4ceff7e5244e334a3fbc5e47e5',
  'name': 'Apis cerana',
  'rank': 'Species'},
 {'id': 'e1d4cbf3872c6c310b7a1c17ddd00ebc',
  'name': 'Apis dorsata',
  'rank': 'Species'}]

Parse names

Parse names using GBIF’s parser API

from pytaxize import gbif
gbif.parse(name=['Arrhenatherum elatius var. elatius',
     'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
   'Vanessa atalanta (Linnaeus, 1758)'])

[{'scientificName': 'Arrhenatherum elatius var. elatius',
  'type': 'SCIENTIFIC',
  'genusOrAbove': 'Arrhenatherum',
  'specificEpithet': 'elatius',
  'infraSpecificEpithet': 'elatius',
  'parsed': True,
  'parsedPartially': False,
  'canonicalName': 'Arrhenatherum elatius elatius',
  'canonicalNameWithMarker': 'Arrhenatherum elatius var. elatius',
  'canonicalNameComplete': 'Arrhenatherum elatius var. elatius',
  'rankMarker': 'var.'},
 {'scientificName': 'Secale cereale subsp. cereale',
  'type': 'SCIENTIFIC',
  ...

Contributors

• Scott Chamberlain

• Colin Talbert

• akshayah3

• panks

• Yanghao Li

• Ben Morris

• Bishakh Ghosh

• Yoav Ram

Meta

• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

• License: MIT; see LICENSE file

Changelog

0.7.0 (2020-06-15)

• first release to pypi