This is a port of the R package taxize, found at ropensci/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.
I usually use Python 2.x locally, but I've just been working on making pytaxize compatible with 2.x and 3.x. Please let me know if anything is broken on either version.
sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize
# python or ipython, etc.
import pytaxizeI'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.
res = pytaxize.Ids('Poa annua', db='col')
res.get_colid()[19275187]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',
...cutoffout = pytaxize.scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf')
out['data'].head() identifiedName offsetEnd offsetStart scientificName verbatim
0 Waxiella 14 7 Waxiella Waxiella
1 W. africana 395 385 Waxiella africana W. africana
2 W. egbara 581 573 Waxiella egbara W. egbara
3 W. erithraeus 771 759 Waxiella erithraeus W. erithraeus
4 W. gwaai 951 944 Waxiella gwaai W. gwaaipytaxize.getacceptednamesfromtsn('208527')
'208527'pytaxize.getcommentdetailfromtsn(tsn=180543)
comment \
0 Status: CITES - Appendix I as U. arctos (Mexic...
1 Comments: Reviewed by Erdbrink (1953), Couturi...
commentator commid commtime updatedate
0 Wilson & Reeder, eds. (2005) 18556 2007-08-20 15:06:38.0 2014-02-03
1 Wilson & Reeder, eds. (2005) 18557 2007-08-20 15:06:38.0 2014-02-03pytaxize.gethierarchyupfromtsn(tsn = 36485)
author parentName parentTsn rankName taxonName tsn
0 Raf. Asteraceae 35420 Genus Agoseris 36485pytaxize.col_children(name=["Apis"])[ id name rank
0 6971712 Apis andreniformis Species
1 6971713 Apis cerana Species
2 6971714 Apis dorsata Species
3 6971715 Apis florea Species
4 6971716 Apis koschevnikovi Species
5 6845885 Apis mellifera Species
6 6971717 Apis nigrocincta Species]Parse names using GBIF's parser API
pytaxize.gbif_parse(scientificname=['Arrhenatherum elatius var. elatius',
'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale','Vanessa atalanta (Linnaeus, 1758)']) authorsParsed bracketAuthorship bracketYear canonicalName \
0 True NaN NaN Arrhenatherum elatius elatius
1 True NaN NaN Secale cereale cereale
2 True NaN NaN Secale cereale cereale
3 True Linnaeus 1758 Vanessa atalanta
canonicalNameComplete canonicalNameWithMarker \
0 Arrhenatherum elatius var. elatius Arrhenatherum elatius var. elatius
1 Secale cereale subsp. cereale Secale cereale subsp. cereale
2 Secale cereale subsp. cereale Secale cereale subsp. cereale
3 Vanessa atalanta (Linnaeus, 1758) Vanessa atalanta
genusOrAbove infraSpecificEpithet rankMarker \
0 Arrhenatherum elatius var.
1 Secale cereale subsp.
2 Secale cereale subsp.
3 Vanessa NaN NaN
scientificName specificEpithet type
0 Arrhenatherum elatius var. elatius elatius WELLFORMED
1 Secale cereale subsp. cereale cereale WELLFORMED
2 Secale cereale ssp. cereale cereale SCINAME
3 Vanessa atalanta (Linnaeus, 1758) atalanta WELLFORMEDnot working yet...
This code is released under the MIT license; please see LICENSE for more details.
- Tests: Some tests have been written, need much more
- Make compatible with Python 2 and 3
- Most functions in the R library
taxizeare still not here yet...