I’ve been working on a Python port of the R package taxize that I maintain. It’s still early days with this Python library, I’d love to know what people think. For example, I’m giving back Pandas DataFrame’s from most functions. Does this make sense?
Installation
sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize
Or git clone the repo down, and python setup.py build && python setup.py install
Load library
import pytaxize
ITIS ping
pytaxize.itis_ping()
'This is the ITIS Web Service, providing access to the data behind www.itis.gov. The database contains 665,266 scientific names (501,207 of them valid/accepted) and 122,735 common names.'
Get hierarchy down from tsn
pytaxize.gethierarchydownfromtsn(tsn = 161030)
tsn rankName taxonName parentName parentTsn
0 161048 Class Sarcopterygii Osteichthyes 161030
1 161061 Class Actinopterygii Osteichthyes 161030
Get hierarchy up from tsn
pytaxize.gethierarchyupfromtsn(tsn = 37906)
author parentName parentTsn rankName taxonName tsn
0 Gaertn. ex Schreb. Asteraceae 35420 Genus Liatris 37906
Get rank names
pytaxize.getranknames()
kingdomname rankid rankname
0 Bacteria 10 Kingdom
1 Bacteria 20 Subkingdom
2 Bacteria 30 Phylum
3 Bacteria 40 Subphylum
4 Bacteria 50 Superclass
5 Bacteria 60 Class
6 Bacteria 70 Subclass
7 Bacteria 80 Infraclass
8 Bacteria 90 Superorder
9 Bacteria 100 Order
10 Bacteria 110 Suborder
11 Bacteria 120 Infraorder
12 Bacteria 130 Superfamily
13 Bacteria 140 Family
14 Bacteria 150 Subfamily
15 Bacteria 160 Tribe
16 Bacteria 170 Subtribe
17 Bacteria 180 Genus
18 Bacteria 190 Subgenus
19 Bacteria 220 Species
20 Bacteria 230 Subspecies
21 Protozoa 10 Kingdom
22 Protozoa 20 Subkingdom
23 Protozoa 25 Infrakingdom
24 Protozoa 30 Phylum
25 Protozoa 40 Subphylum
26 Protozoa 45 Infraphylum
27 Protozoa 47 Parvphylum
28 Protozoa 50 Superclass
29 Protozoa 60 Class
.. ... ... ...
150 Chromista 190 Subgenus
151 Chromista 200 Section
152 Chromista 210 Subsection
153 Chromista 220 Species
154 Chromista 230 Subspecies
155 Chromista 240 Variety
156 Chromista 250 Subvariety
157 Chromista 260 Form
158 Chromista 270 Subform
159 Archaea 10 Kingdom
160 Archaea 20 Subkingdom
161 Archaea 30 Phylum
162 Archaea 40 Subphylum
163 Archaea 50 Superclass
164 Archaea 60 Class
165 Archaea 70 Subclass
166 Archaea 80 Infraclass
167 Archaea 90 Superorder
168 Archaea 100 Order
169 Archaea 110 Suborder
170 Archaea 120 Infraorder
171 Archaea 130 Superfamily
172 Archaea 140 Family
173 Archaea 150 Subfamily
174 Archaea 160 Tribe
175 Archaea 170 Subtribe
176 Archaea 180 Genus
177 Archaea 190 Subgenus
178 Archaea 220 Species
179 Archaea 230 Subspecies
Search by scientific name
pytaxize.searchbyscientificname(x="Tardigrada")
combinedname tsn
0 Rotaria tardigrada 58274
1 Notommata tardigrada 58898
2 Pilargis tardigrada 65562
3 Tardigrada 155166
4 Heterotardigrada 155167
5 Arthrotardigrada 155168
6 Mesotardigrada 155358
7 Eutardigrada 155362
8 Scytodes tardigrada 866744
Get accepted names from tsn
pytaxize.getacceptednamesfromtsn('208527')
If accepted, returns the same id
'208527'
More
For the other functions see https://github.com/sckott/pytaxize/blob/master/pytaxize/itis.py