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
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.