def loadH2007():
h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')
# 2014-04-08 Misspelling
if h2007.maybeTaxon('Chaetothryriomycetidae') != None:
h2007.taxon('Chaetothryriomycetidae').rename('Chaetothyriomycetidae')
if h2007.maybeTaxon('Asteriniales') != None:
h2007.taxon('Asteriniales').rename('Asterinales')
else:
h2007.taxon('Asterinales').synonym('Asteriniales')
return h2007
def load_h2007():
h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')
# 2014-04-08 Misspelling
if h2007.maybeTaxon('Chaetothryriomycetidae') != None:
h2007.taxon('Chaetothryriomycetidae').rename('Chaetothyriomycetidae')
if h2007.maybeTaxon('Asteriniales') != None:
h2007.taxon('Asteriniales').rename('Asterinales')
else:
h2007.taxon('Asterinales').synonym('Asteriniales')
# h2007/if synonym https://github.com/OpenTreeOfLife/reference-taxonomy/issues/40
h2007.taxon('Urocystales').synonym('Urocystidales')
return h2007
def load_h2007():
h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')
# 2014-04-08 Misspelling
if h2007.maybeTaxon('Chaetothryriomycetidae') != None:
h2007.taxon('Chaetothryriomycetidae').rename('Chaetothyriomycetidae')
if h2007.maybeTaxon('Asteriniales') != None:
h2007.taxon('Asteriniales').rename('Asterinales')
else:
h2007.taxon('Asterinales').synonym('Asteriniales')
# h2007/if synonym https://github.com/OpenTreeOfLife/reference-taxonomy/issues/40
h2007.taxon('Urocystales').synonym('Urocystidales')
return h2007
ott.absorb(silva)
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/30
# https://github.com/OpenTreeOfLife/feedback/issues/5
for name in [
'GAL08', 'GOUTA4', 'JL-ETNP-Z39', 'Kazan-3B-28', 'LD1-PA38', 'MVP-21',
'NPL-UPA2', 'OC31', 'RsaHF231', 'S2R-29', 'SBYG-2791', 'SM2F11',
'WCHB1-60', 'T58', 'LKM74', 'LEMD255', 'CV1-B1-93', 'H1-10', 'H26-1',
'M1-18D08', 'D4P07G08', 'DH147-EKD10', 'LG25-05', 'NAMAKO-1',
'RT5iin25', 'SA1-3C06', 'DH147-EKD23'
]:
ott.taxon(name).elide()
# ----- Hibbett 2007 updated upper fungal taxonomy -----
h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')
# 2014-04-08 Misspelling
h2007.taxon('Chaetothryriomycetidae').rename('Chaetothyriomycetidae')
ott.absorb(h2007)
# h2007/if synonym https://github.com/OpenTreeOfLife/reference-taxonomy/issues/40
ott.taxon('Urocystales').synonym('Urocystidales')
# ----- Index Fungorum -----
# IF is pretty comprehensive for Fungi, but has an assortment of other
# things, mostly eukaryotic microbes. We should treat the former as
# more authoritative than NCBI, and the latter as less authoritative
# than NCBI.
# Jython script to build the Open Tree reference taxonomy
from org.opentreeoflife.smasher import Taxonomy
import sys
sys.path.append("feed/ott/")
from chromista_spreadsheet import fixChromista
ott = Taxonomy.newTaxonomy()
h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')
ott.absorb(h2007)
silva = Taxonomy.getTaxonomy('tax/silva/', 'silva')
ott.absorb(silva)
study713 = Taxonomy.getTaxonomy('tax/713/', 'study713')
ott.notSame(study713.taxon('Buchnera'), silva.taxon('Buchnera'))
ott.absorb(study713)
fung = Taxonomy.getTaxonomy('tax/if/', 'if')
fung.smush()
fung.analyzeMajorRankConflicts()
ott.absorb(fung)
ncbi = Taxonomy.getTaxonomy('tax/ncbi/', 'ncbi')
ncbi.taxon('Fungi').hideDescendants()
ott.same(ncbi.taxon('Cyanobacteria'), silva.taxon('D88288/#3'))
ott.notSame(ncbi.taxon('Burkea'), fung.taxon('Burkea'))
ott.notSame(ncbi.taxon('Coscinium'), fung.taxon('Coscinium'))
ott.notSame(ncbi.taxon('Perezia'), fung.taxon('Perezia'))
# This one should be temporary, might change with SILVA 117.
