pytaxize

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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

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.

Installation

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

python or ipython, etc.

import 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.

res = pytaxize.Ids('Poa annua', db='col')
res.get_colid()
[19275187]

Scrape taxonomic names

out = 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. gwaai

ITIS low level functions

pytaxize.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  2014-02-03
pytaxize.gethierarchyupfromtsn(tsn = 36485)

  author  parentName parentTsn rankName taxonName    tsn
0   Raf.  Asteraceae     35420    Genus  Agoseris  36485

Catalogue of Life

pytaxize.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

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  WELLFORMED

Get random vector of taxon names

_not working yet..._

Meta

License

MIT

Indices and tables