silva = taxonomies.loadSilva()

# - Deal with parent/child homonyms in SILVA -

# Arbitrary choices here to eliminate ambiguities down the road when NCBI gets merged.

# (If the homonym is retained, then the merge algorithm will have no

# way to choose between them, and refuse to match either. It will

# then create a third homonym.)

# Note order dependence between the following two

silva.taxon('Intramacronucleata','Intramacronucleata').rename('Intramacronucleata inf.')

silva.taxon('Spirotrichea','Intramacronucleata inf.').rename('Spirotrichea inf.')

silva.taxon('Cyanobacteria','Bacteria').rename('Cyanobacteria sup.')

silva.taxon('Actinobacteria','Bacteria').rename('Actinobacteria sup.')

silva.taxon('Acidobacteria','Bacteria').rename('Acidobacteria sup.')

silva.taxon('Ochromonas','Ochromonadales').rename('Ochromonas sup.')

silva.taxon('Tetrasphaera','Tetrasphaera').rename('Tetrasphaera inf.')

# SILVA's placement of Rozella as a sibling of Fungi is contradicted

# by Hibbett 2007, which puts it under Fungi. Hibbett gets priority.

# We make the change to SILVA to prevent Nucletmycea from being

# labeled 'tattered'.

silva.taxon('Fungi').take(silva.taxon('Rozella'))

# 2014-04-12 Rick Ree #58 and #48 - make them match NCBI

silva.taxon('Arthrobacter Sp. PF2M5').rename('Arthrobacter sp. PF2M5')

silva.taxon('Halolamina sp. wsy15-h1').rename('Halolamina sp. WSY15-H1')

# RR #55 - this is a silva/ncbi homonym

silva.taxon('vesicomya').rename('Vesicomya')

# From Laura and Dail on 5 Feb 2014

# https://groups.google.com/forum/#!topic/opentreeoflife/a69fdC-N6pY

silva.taxon('Diatomea').rename('Bacillariophyta')

# 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']:

silva.taxon(name).elide() #maybe just hide instead ?

# - Deal with division alignment issues -

ott.notSame(silva.taxon('Ctenophora', 'Coscinodiscophytina'),

skel.taxon('Ctenophora'))

ott.markDivisions(silva)

taxonomies.checkDivisions(silva)

ott.absorb(silva)

h2007 = taxonomies.loadH2007()

ott.absorb(h2007)

# h2007/if synonym https://github.com/OpenTreeOfLife/reference-taxonomy/issues/40

ott.taxon('Urocystales').synonym('Urocystidales')

allfung = taxonomies.loadFung()

print "Index Fungorum has %s nodes"%allfung.count()

# JAR 2014-04-27 JAR found while investigating 'hidden' status of

# Thelohania butleri. Move out of Protozoa to prevent their being hidden

allfung.taxon('Fungi').take(allfung.taxon('Microsporidia'))

# *** Non-Fungi processing

# JAR 2014-05-13 Chlorophyte or fungus? This one is very confused.

# Pick it up from GBIF if at all

allfung.taxon('Byssus phosphorea').prune()

if False: # see taxonomies.loadFung

# Work in progress. By promoting to root we've lost the fact that

# protozoa are eukaryotes, which is unfortunate. Not important in this

# case, but suggestive of deeper problems in the framework.

# Test case: Oomycota should end up in Stramenopiles.

fung_Protozoa = allfung.maybeTaxon('Protozoa')

if fung_Protozoa != None:

fung_Protozoa.hide() # recursive

fung_Protozoa.detach()

fung_Protozoa.elide()

fung_Chromista = allfung.maybeTaxon('Chromista')

if fung_Chromista != None:

fung_Chromista.hide() # recursive

fung_Chromista.detach()

fung_Chromista.elide()

# IF Thraustochytriidae = SILVA Thraustochytriaceae ? (Stramenopiles)

# IF T. 90638 contains Sicyoidochytrium, Schizochytrium, Ulkenia, Thraustochytrium

# Parietichytrium, Elina, Botryochytrium, Althornia

# SILVA T. contains Ulkenia and a few others of these... I say yes.

thraust = allfung.taxon('90377')

thraust.synonym('Thraustochytriaceae')

thraust.synonym('Thraustochytriidae')

thraust.synonym('Thraustochytridae')

# IF Labyrinthulaceae = SILVA Labyrinthulomycetes ? NO.

# IF L. contains only Labyrinthomyxa, Labyrinthula

# SILVA L. contains a lot more than that.

# IF Hyphochytriaceae = SILVA Hyphochytriales ?

# SILVA Hyphochytriales = AB622284/#4 contains only

# Hypochitrium, Rhizidiomycetaceae

# There are two Bacillaria.

# 1. NCBI 3002, in Stramenopiles, contains Bacillaria paxillifer.

# No synonyms in NCBI.

# IF has Bacillaria as a synonym for Camillea (if:777).

# Bacillaria is not otherwise in IF.

# Cammillea in IF is in Stramenopiles.

# 2. NCBI 109369, in Pezizomycotina

# No synonyms in NCBI.

# NCBI 13677 = Camillea, a fish.

# There are two Polyangium, a bacterium (NCBI) and a flatworm (IF).

# smush folds sibling taxa that have the same name.

# (repeats - see loadFung() ???)

allfung.smush()

# *** Fungi processing

print "Fungi in Index Fungorum has %s nodes"%allfung.taxon('Fungi').count()

# fung = allfung.select(allfung.taxon('Fungi'))

# SIDE EFFECT. Ideally there would be a declarative

# (non-side-effecty) way to do this.

# allfung.taxon('Fungi').trim()

# Revert to previous method for the time being due to large chunks of Fungi

# lacking parent links

fung = allfung

# JAR 2014-04-11 Missing in earlier IF, mistake in later IF -

# extraneous authority string. See Romina's issue #42

# This is a fungus.

cyph = fung.maybeTaxon('Cyphellopsis')

if cyph == None:

cyph = fung.maybeTaxon('Cyphellopsis Donk 1931')

if cyph != None:

cyph.rename('Cyphellopsis')

else:

cyph = fung.newTaxon('Cyphellopsis', 'genus', 'if:17439')

fung.taxon('Niaceae').take(cyph)

# 2014-03-07 Prevent a false match

# https://groups.google.com/d/msg/opentreeoflife/5SAPDerun70/fRjA2M6z8tIJ

# This is a fungus in Pezizomycotina

ott.notSame(silva.taxon('Phaeosphaeria'), fung.taxon('Phaeosphaeria'))

# 2014-04-08 This was causing Agaricaceae to be paraphyletic

ott.notSame(silva.taxon('Morganella'), fung.taxon('Morganella'))

# 2014-04-08 More IF/SILVA bad matches

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/63

for name in ['Trichoderma harzianum', # in Pezizomycotina

'Acantharia', # in Pezizomycotina

'Bogoriella', # in Pezizomycotina

'Steinia', # in Pezizomycotina

'Sclerotinia homoeocarpa', # in Pezizomycotina

'Epiphloea', # in Pezizomycotina

'Campanella', # in Agaricomycotina

'Lacrymaria', # in Agaricomycotina

'Frankia', # in Pezizomycotina / bacterium in SILVA

'Phialina', # in Pezizomycotina

'Puccinia triticina']: # in Pucciniomycotina in Fungi

ott.notSame(silva.taxon(name), fung.taxon(name))

# Romina 2014-04-09

# IF has both Hypocrea and Trichoderma. Hypocrea is the right name.

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

fung.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type

fung.taxon('Hypocrea').absorb(fung.taxonThatContains('Trichoderma', 'Hypocrea rufa'))

# Romina https://github.com/OpenTreeOfLife/reference-taxonomy/issues/42

fung.taxon('Trichoderma deliquescens').rename('Hypocrea lutea')

# 2014-04-25 JAR

# There are three Bostrychias: a rhodophyte, a fungus, and a bird.

# The fungus name is a synonym for Cytospora.

if fung.maybeTaxon('Bostrychia', 'Ascomycota') != None:

ott.notSame(silva.taxon('Bostrychia', 'Rhodophyceae'), fung.taxon('Bostrychia', 'Ascomycota'))

# analyzeMajorRankConflicts sets the "major_rank_conflict" flag when

# intermediate ranks are missing (e.g. a family that's a child of a

# class)

fung.analyzeMajorRankConflicts()

ott.absorb(fung)

print "Fungi in h2007 + if has %s nodes"%ott.taxon('Fungi').count()

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/20

# Problem: Chlamydotomus is an incertae sedis child of Fungi. Need to

# find a good home for it.

#

# Mycobank says Chlamydotomus beigelii = Trichosporon beigelii:

# http://www.mycobank.org/BioloMICS.aspx?Link=T&TableKey=14682616000000067&Rec=35058&Fields=All

#

# IF says the basionym is Pleurococcus beigelii, and P. beigelii's current name

# is Geotrichum beigelii. IF says the type for Trichosporon is Trichosporon beigelii,

# and that T. beigelii's current name is Trichosporum beigelii... with no synonymies...

# So IF does not corroborate Mycobank.

#

# So we could consider absorbing Chlamydotomus into Trichosoporon. But...

#

# Not sure about this. beigelii has a sister, cellaris, that should move along

# with it, but the name Trichosporon cellaris has never been published.

# Cb = ott.taxon('Chlamydotomus beigelii')

# Cb.rename('Trichosporon beigelii')

# ott.taxon('Trichosporon').take(Cb)

#

# Just make it incertae sedis and put off dealing with it until someone cares...

# 2014-04-13 Romina #40, #60

for foo in [('Neozygitales', ['Neozygitaceae']),

('Asteriniales', ['Asterinaceae']),

('Savoryellales', ['Savoryella', 'Ascotaiwania', 'Ascothailandia']),

('Cladochytriales', ['Cladochytriaceae', 'Nowakowskiellaceae', 'Septochytriaceae', 'Endochytriaceae']),

('Jaapiales', ['Jaapiaceae']),

('Coniocybales', ['Coniocybaceae']),

('Hyaloraphidiales', ['Hyaloraphidiaceae']),

('Mytilinidiales', ['Mytilinidiaceae', 'Gloniaceae'])]:

order = ott.taxon(foo[0])

for family in foo[1]:

order.take(ott.taxon(family))

# ** No taxon found with this name: Nowakowskiellaceae

# ** No taxon found with this name: Septochytriaceae

# ** No taxon found with this name: Jaapiaceae

# ** (null=if:81865 Rhizocarpaceae) is already a child of (null=h2007:212 Rhizocarpales)

# ** No taxon found with this name: Hyaloraphidiaceae

ncbi = taxonomies.loadNcbi()

ncbi.taxon('Viruses').hide()

# David Hibbett has requested that for Fungi, only Index Fungorum

# should be seen. Rather than delete the NCBI fungal taxa, we just

# mark them 'hidden' so they can be suppressed downstream. This

# preserves the identifier assignments, which may have been used

# somewhere.

ncbi.taxon('Fungi').hideDescendantsToRank('species')

# - Touch-up -

# RR 2014-04-12 #49

ncbi.taxon('leotiomyceta').rename('Leotiomyceta')

# RR #53

ncbi.taxon('White-sloanea').synonym('White-Sloanea')

# RR #56

ncbi.taxon('sordariomyceta').rename('Sordariomyceta')

# RR #52

ncbi.taxon('spinocalanus spinosus').rename('Spinocalanus spinosus')

ncbi.taxon('spinocalanus angusticeps').rename('Spinocalanus angusticeps')

# RR #59

ncbi.taxon('candidate division SR1').rename('Candidate division SR1')

ncbi.taxon('candidate division WS6').rename('Candidate division WS6')

ncbi.taxon('candidate division BRC1').rename('Candidate division BRC1')

ncbi.taxon('candidate division OP9').rename('Candidate division OP9')

ncbi.taxon('candidate division JS1').rename('Candidate division JS1')

# RR #51

ncbi.taxon('Dendro-hypnum').synonym('Dendro-Hypnum')

# RR #45

ncbi.taxon('Cyrto-hypnum').synonym('Cyrto-Hypnum')

# RR #54

ncbi.taxon('Sciuro-hypnum').synonym('Sciuro-Hypnum')

# RR 2014-04-12 #46

ncbi.taxon('Pechuel-loeschea').synonym('Pechuel-Loeschea')

# RR #50

ncbi.taxon('Saxofridericia').synonym('Saxo-Fridericia')

ncbi.taxon('Saxofridericia').synonym('Saxo-fridericia')

# RR #57

ncbi.taxon('Solms-laubachia').synonym('Solms-Laubachia')

# Romina 2014-04-09

# NCBI has both Hypocrea and Trichoderma.

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

ncbi.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type

ncbi.taxon('Hypocrea').absorb(ncbi.taxonThatContains('Trichoderma', 'Hypocrea rufa'))

# - Alignment to OTT -

#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'))

# JAR 2014-04-11 Discovered during regression testing

ott.notSame(ncbi.taxon('Epiphloea', 'Rhodophyta'), fung.taxon('Epiphloea', 'Ascomycota'))

# JAR attempt to resolve ambiguous alignment of Trichosporon in IF and

# NCBI based on common parent and member.

# Type = T. beigelii, which is current, according to Mycobank.

# But I'm going to use a different 'type', Trichosporon cutaneum.

ott.same(fung.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'), ncbi.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'))

# 2014-04-23 In new version of IF - obvious misalignment

ott.notSame(ncbi.taxon('Crepidula', 'Gastropoda'), fung.taxon('Crepidula', 'Microsporidia'))

ott.notSame(ncbi.taxon('Hessea', 'Viridiplantae'), fung.taxon('Hessea', 'Microsporidia'))

# 2014-04-23 Resolve ambiguity introduced into new version of IF

# http://www.speciesfungorum.org/Names/SynSpecies.asp?RecordID=331593

ott.same(ncbi.taxon('Gymnopilus spectabilis var. junonius'), fung.taxon('Gymnopilus junonius'))

# JAR 2014-04-23 More sample contamination in SILVA 115

ott.same(ncbi.taxon('Lamprospora'), fung.taxon('Lamprospora'))

# JAR 2014-04-25

ott.notSame(silva.taxon('Bostrychia', 'Rhodophyceae'), ncbi.taxon('Bostrychia', 'Aves'))

ott.absorb(ncbi)

gbif = taxonomies.loadGbif()

gbif.taxon('Viruses').hide()

# Fungi suppressed at David Hibbett's request

gbif.taxon('Fungi').hideDescendantsToRank('species')

# Microbes suppressed at Laura Katz's request

gbif.taxon('Bacteria','life').hideDescendants()

gbif.taxon('Archaea','life').hideDescendants()

# Paraphyletic - now taken care of in loadGbif

if False:

gbif_Protozoa = gbif.taxon('Protozoa')

gbif_Protozoa.hide() # recursive

if False:

gbif_Protozoa.detach()

gbif_Protozoa.elide()

gbif_Chromista = gbif.taxon('Chromista')

gbif_Chromista.hide() # recursive

if False:

gbif_Chromista.detach()

gbif_Chromista.elide()

# - Touch-up -

# Rod Page blogged about this one

# http://iphylo.blogspot.com/2014/03/gbif-liverwort-taxonomy-broken.html

gbif.taxon('Jungermanniales','Marchantiophyta').absorb(gbif.taxon('Jungermanniales','Bryophyta'))

# Joseph 2013-07-23 https://github.com/OpenTreeOfLife/opentree/issues/62

# GBIF has two copies of Myospalax

gbif.taxon('6006429').absorb(gbif.taxon('2439119'))

# RR 2014-04-12 #47

gbif.taxon('Drake-brockmania').absorb(gbif.taxon('Drake-Brockmania'))

# RR #50 - this one is in NCBI, see above

gbif.taxon('Saxofridericia').absorb(gbif.taxon('4930834')) #Saxo-Fridericia

# RR #57 - the genus is in NCBI, see above

gbif.taxon('Solms-laubachia').absorb(gbif.taxon('4908941')) #Solms-Laubachia

gbif.taxon('Solms-laubachia pulcherrima').absorb(gbif.taxon('Solms-Laubachia pulcherrima'))

# RR #45

gbif.taxon('Cyrto-hypnum').absorb(gbif.taxon('4907605'))

# 2014-04-13 JAR noticed while grepping

gbif.taxon('Chryso-hypnum').absorb(gbif.taxon('Chryso-Hypnum'))

gbif.taxon('Drepano-Hypnum').rename('Drepano-hypnum')

gbif.taxon('Complanato-Hypnum').rename('Complanato-hypnum')

gbif.taxon('Leptorrhyncho-Hypnum').rename('Leptorrhyncho-hypnum')

# Romina 2014-04-09

# GBIF has both Hypocrea and Trichoderma. And it has four Trichoderma synonyms...

# pick the one that contains bogo-type Hypocrea rufa

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

gbif.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type

gbif.taxon('Hypocrea').absorb(gbif.taxonThatContains('Trichoderma', 'Hypocrea rufa'))

# 2014-04-21 RR

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/45

for epithet in ['cylindraceum',

'lepidoziaceum',

'intermedium',

'espinosae',

'pseudoinvolvens',

'arzobispoae',

'sharpii',

'frontinoae',

'atlanticum',

'stevensii',

'brachythecium']:

gbif.taxon('Cyrto-hypnum ' + epithet).absorb(gbif.taxon('Cyrto-Hypnum ' + epithet))

# JAR 2014-04-23 Noticed while perusing silva/gbif conflicts

gbif.taxon('Ebriaceae').synonym('Ebriacea')

gbif.taxon('Acanthocystidae').absorb(gbif.taxon('Acanthocistidae'))

gbif.taxon('Dinophyta').synonym('Dinoflagellata')

# JAR 2014-06-29 stumbled on this while trying out new alignment

# methods and examining troublesome homonym Bullacta exarata.

# GBIF obviously puts it in the wrong place, see description at

# http://www.gbif.org/species/4599744 (it's a snail, not a shrimp).

bex = gbif.taxon('Bullacta exarata', 'Atyidae')

bec = gbif.taxon('Bullacta ecarata', 'Atyidae')

if bex != None and bec != None:

bex.absorb(bec)

bex.detach()

# - Alignment -

#ott.same(gbif.taxon('Cyanobacteria'), silva.taxon('Cyanobacteria','Cyanobacteria')) #'D88288/#3'

# Automatic alignment makes the wrong choice for the following two

ott.same(ncbi.taxon('5878'), gbif.taxon('10')) # Ciliophora gbif:3269382

ott.same(ncbi.taxon('29178'), gbif.taxon('389')) # Foraminifera gbif:4983431

# Tetrasphaera is a messy multi-way homonym

ott.same(ncbi.taxon('Tetrasphaera','Intrasporangiaceae'), gbif.taxon('Tetrasphaera','Intrasporangiaceae'))

# SILVA's Retaria is in SAR, GBIF's is in Brachiopoda

ott.notSame(silva.taxon('Retaria'), gbif.taxon('Retaria'))

# Bad alignments to NCBI

ott.notSame(ncbi.taxon('Labyrinthomorpha'), gbif.taxon('Labyrinthomorpha'))

ott.notSame(ncbi.taxon('Ophiurina'), gbif.taxon('Ophiurina','Ophiurinidae'))

ott.notSame(ncbi.taxon('Rhynchonelloidea'), gbif.taxon('Rhynchonelloidea'))

ott.notSame(ncbi.taxon('Neoptera'), gbif.taxon('Neoptera', 'Diptera'))

ott.notSame(gbif.taxon('6101461'), ncbi.taxon('Tipuloidea')) # genus Tipuloidea

ott.notSame(silva.taxon('GN013951'), gbif.taxon('Gorkadinium')) #Tetrasphaera

# Rick Ree 2014-03-28 https://github.com/OpenTreeOfLife/reference-taxonomy/issues/37

ott.same(ncbi.taxon('Calothrix', 'Rivulariaceae'), gbif.taxon('Calothrix', 'Rivulariaceae'))

ott.same(ncbi.taxon('Chlorella', 'Chlorellaceae'), gbif.taxon('Chlorella', 'Chlorellaceae'))

ott.same(ncbi.taxon('Myrmecia', 'Microthamniales'), gbif.taxon('Myrmecia', 'Microthamniales'))

# JAR 2014-04-18 attempt to resolve ambiguous alignment of

# Trichosporon in IF and GBIF based on common member

ott.same(fung.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'), gbif.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'))

# Obviously the same genus, can't tell what's going on

ott.same(gbif.taxon('Hygrocybe'), fung.taxon('Hygrocybe'))

# JAR 2014-04-23 More sample contamination in SILVA 115

ott.same(gbif.taxon('Lamprospora'), fung.taxon('Lamprospora'))

# JAR 2014-04-23 IF update fallout

ott.same(gbif.taxonThatContains('Penicillium', 'Penicillium expansum'), fung.taxonThatContains('Penicillium', 'Penicillium expansum'))

# In GBIF, if a rank is skipped for some children but not others, that

# means rank-skipped children are incertae sedis. Mark them so.

gbif.analyzeMajorRankConflicts()

ott.absorb(gbif)

irmng = taxonomies.loadIrmng()

irmng.taxon('Viruses').hide()

# JAR 2014-04-26 Flush all 'Unaccepted' taxa

irmng.taxon('Unaccepted', 'life').prune()

# Fungi suppressed at David Hibbett's request

irmng.taxon('Fungi').hideDescendantsToRank('species')

# Neopithecus (extinct) occurs in two places. Flush one, mark the other

irmng.taxon('1413316').prune() #Neopithecus in Mammalia

irmng.taxon('1413315').extinct() #Neopithecus in Primates (Pongidae)

ott.same(gbif.taxon('3172047'), irmng.taxon('1381293')) # Veronica

ott.same(gbif.taxon('6101461'), irmng.taxon('1170022')) # genus Tipuloidea (not superfamily)

# IRMNG has four Tetrasphaeras.

ott.same(ncbi.taxon('Tetrasphaera','Intrasporangiaceae'), irmng.taxon('Tetrasphaera','Intrasporangiaceae'))

ott.same(gbif.taxon('Gorkadinium','Dinophyceae'), irmng.taxon('Gorkadinium','Dinophyceae'))

# Microbes suppressed at Laura Katz's request

irmng.taxon('Bacteria','life').hideDescendants()

irmng.taxon('Archaea','life').hideDescendants()

# RR #50

# irmng.taxon('Saxo-Fridericia').rename('Saxofridericia')

# irmng.taxon('Saxofridericia').absorb(irmng.taxon('Saxo-fridericia'))

saxo = irmng.maybeTaxon('1063899')

if saxo != None:

saxo.absorb(irmng.taxon('1071613'))

# Romina 2014-04-09

# IRMNG has EIGHT different Trichodermas. (Four are synonyms of other things.)

# 1307461 = Trichoderma Persoon 1794, in Hypocreaceae

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

irmng.taxon('Hypocrea').absorb(irmng.taxon('1307461'))

# JAR 2014-04-18 attempt to resolve ambiguous alignment of

# Trichosporon in IF and IRMNG based on common parent and member

ott.same(fung.taxon('Trichosporon'), irmng.taxon('Trichosporon'))

# JAR 2014-04-24 false match

ott.notSame(irmng.taxon('Protaspis', 'Chordata'), ncbi.taxon('Protaspis', 'Cercozoa'))

# JAR 2014-04-18 while investigating hidden status of Coscinodiscus radiatus

ott.notSame(irmng.taxon('Coscinodiscus', 'Porifera'), ncbi.taxon('Coscinodiscus', 'Stramenopiles'))

# Protista is paraphyletic

if False:

irmng_Protista = irmng.taxon('Protista','life')

irmng_Protista.hide()

if False:

irmng_Protista.detach()

irmng_Protista.elide()

irmng.analyzeMajorRankConflicts()

ott.absorb(irmng)