Package: pytaxize
pytaxizeThis is a port of the R packagetaxize.  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 oftaxizewill be for those that are pythonistas at heart. Also, you could usepytaxizein a web app, whereas you could withtaxize(e.g., in a Shiny app), but it wouldn’t scale, be very fast, etc.python 2/3pytaxize is only developed in and tested with Python 3InstallationStable from pypipip install pytaxizeDevelopment versionsudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxizeTaxonomic IdsI’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.frompytaxizeimportIdsres=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 searchimportpytaxizepytaxize.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 namesout=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 functionsfrompytaxizeimportitisitis.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 Lifefrompytaxizeimportcolx=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 namesParse names using GBIF’s parser APIfrompytaxizeimportgbifgbif.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',...ContributorsScott ChamberlainColin Talbertakshayah3panksYanghao LiBen MorrisBishakh GhoshYoav RamMetaPlease note that this project is released with aContributor Code of Conduct. By participating in this project you agree to abide by its terms.License: MIT; seeLICENSE fileChangelog0.7.0 (2020-06-15)first release to pypi