ott = UnionTaxonomy.newTaxonomy()

# There ought to be tests for all of these...

for name in names_of_interest:

ott.eventlogger.namesOfInterest.add(name)

# When lumping, prefer to use ids that have been used in OTU matching

# This list could be used for all sorts of purposes...

ott.loadPreferredIds('ids-that-are-otus.tsv', False)

ott.loadPreferredIds('ids-in-synthesis.tsv', True)

ott.setSkeleton(Taxonomy.getTaxonomy('tax/skel/', 'skel'))

silva = prepare_silva(ott)

ott.absorb(silva)

check_invariants(ott)

h2007 = prepare_h2007(ott)

ott.absorb(h2007)

(fungi, fungorum_sans_fungi) = prepare_fungorum(ott)

ott.absorb(fungi)

check_invariants(ott)

# the non-Fungi from Index Fungorum get absorbed below

lamiales = prepare_lamiales(ott)

ott.absorb(lamiales)

(malacostraca, worms_sans_malacostraca) = prepare_worms(ott)

ott.absorb(malacostraca)

ncbi = prepare_ncbi(ott)

align_ncbi_to_silva(ncbi, silva, ott)

ott.absorb(ncbi)

check_invariants(ott)

ott.absorb(worms_sans_malacostraca)

ott.absorb(fungorum_sans_fungi)

gbif = prepare_gbif(ott)

ott.absorb(gbif)

irmng = prepare_irmng(ott)

ott.absorb(irmng)

taxonomies.link_to_h2007(ott)

get_default_extinct_info_from_gbif(gbif, ott)

check_invariants(ott)

# consider try: ... except: print '**** Exception in patch_ott'

patch_ott(ott)

# Experimental...

unextinct_ncbi(ncbi, ott)

# Remove all trees but the largest (or make them life incertae sedis)

ott.deforestate()

# -----------------------------------------------------------------------------

# OTT id assignment

# Force some id assignments... will try to automate this in the future.

# Most of these come from looking at the otu-deprecated.tsv file after a

# series of smasher runs.

for (inf, sup, id) in [

('Tipuloidea', 'Diptera', '722875'),

('Saccharomycetes', 'Saccharomycotina', '989999'),

('Phaeosphaeria', 'Ascomycota', '5486272'),

('Synedra acus','Eukaryota','992764'),

('Epiphloea','Halymeniaceae','5342325'),

('Hessea','Archaeplastida','600099'),

('Morganella','Arthropoda','6400'),

('Rhynchonelloidea','Rhynchonellidae','5316010'),

('Epiphloea', 'Lichinales', '5342482'),

('Morganella', 'Fungi', '973932'),

('Parmeliaceae', 'Lecanorales', '305904'),

]:

tax = ott.taxon(inf, sup)

if tax != None:

tax.setId(id)

ott.taxonThatContains('Rhynchonelloidea', 'Sphenarina').setId('795939') # NCBI

for (ncbi_id, ott_id, name) in ncbi_assignments_list:

n = ncbi.maybeTaxon(ncbi_id)

if n != None:

im = ott.image(n)

if im != None:

im.setId(ott_id)

else:

print '** NCBI %s not mapped - %s' % (ncbi_id, name)

else:

print '** No NCBI taxon %s - %s' % (ncbi_id, name)

# Cylindrocarpon is now Neonectria

ott.image(gbif.taxon('2563163')).setId('51754')

# Foo

trich = fungi.maybeTaxon('Trichosporon')

if trich != None:

ott.image(trich).setId('364222')

#ott.image(fungi.taxon('11060')).setId('4107132') #Cryptococcus - a total mess

# Assign OTT ids to taxa that don't have them, re-using old ids when possible

ids = Taxonomy.getTaxonomy('tax/prev_ott/')

# Assign old ids to nodes in the new version

ott.assignIds(ids)

report_on_h2007(h2007, ott)

silva = taxonomies.load_silva()

ott.addSource(silva)

# JAR 2014-05-13 scrutinizing pin() and BarrierNodes. Wikipedia

# confirms this synonymy. Dail L. prefers -phyta to -phyceae

# but says -phytina would be more correct per code.

# Skeleton taxonomy has -phyta (on Dail's advice).

silva.taxon('Rhodophyceae').synonym('Rhodophyta') # moot now?

silva.taxon('Florideophycidae', 'Rhodophyceae').synonym('Florideophyceae')

silva.taxon('Stramenopiles', 'SAR').synonym('Heterokonta') # needed by WoRMS

fungorum = taxonomies.load_fung()

ott.addSource(fungorum)

fungi_root = fungorum.taxon('Fungi')

fungi = fungorum.select(fungi_root)

fungi_root.trim()

print "Fungi in Index Fungorum has %s nodes"%fungi.count()

# *** Alignment to SILVA

# 2014-03-07 Prevent a false match

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

# This is a fungus in Pezizomycotina

# ### CHECK: was silva.taxon('Phaeosphaeria')

# ott.notSame(ott.taxon('Phaeosphaeria', 'Rhizaria'), fungi.taxon('Phaeosphaeria', 'Ascomycota'))

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

# ### CHECK: was silva.taxon('Morganella')

# ott.notSame(ott.taxon('Morganella'), fungi.taxon('Morganella'))

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

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

# The notSame directives are unnecessary if SAR is a division

for name in ['Acantharia', # in Venturiaceae < Fungi < Opisth. / Rhizaria < SAR

'Steinia', # in Lecideaceae < Fungi / Alveolata / insect < Holozoa in irmng

'Epiphloea', # in Pezizomycotina < Opisth. / Rhodophyta should be OK, Rh. is a division

'Campanella', # in Agaricomycotina < Nuclet. / SAR / Cnidaria

'Lacrymaria', # in Agaricomycotina / SAR

#'Phialina', # in Pezizomycotina - not in fung

#'Frankia', # in Pezizomycotina / Bacteria - not even in latest fung

'Bogoriella', # in Verrucariaceae < Pezizomycotina < Euk. / Bogoriellaceae < Bacteria should be ok

]:

# ### CHECK: was silva.taxon

ott.notSame(ott.taxon(name), fungi.taxon(name, 'Fungi'))

# Trichoderma harzianum, Sclerotinia homoeocarpa, Puccinia

# triticina are removed from SILVA early

# 2014-04-25 JAR

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

# The fungus name is a synonym for Cytospora.

# ### CHECK: was silva.taxon

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

ott.notSame(ott.taxon('Bostrychia', 'Rhodophyceae'),

fungi.taxon('Bostrychia', 'Ascomycota'))

# 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...

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/79

# ### CHECK: was silva.taxon

ott.notSame(ott.taxon('Podocystis', 'Stramenopiles'), fungi.taxon('Podocystis', 'Fungi'))

# https://github.com/OpenTreeOfLife/feedback/issues/45

if False:

ott.same(fungorum.maybeTaxon('Choanoflagellida'),

ott.maybeTaxon('Choanoflagellida', 'Opisthokonta'))

# Create a homonym (the one in Fungi, not the same as the one in Alveolata)

# so that the IF Ciliophora can map to it

if ott.maybeTaxon('Ciliophora', 'Fungi') == None:

cil = ott.newTaxon('Ciliophora', 'genus', 'if:7660')

cil.setId('5343665')

ott.taxon('Fungi').take(cil)

cil.incertaeSedis()

# Create a homonym (the one in Fungi, not the same as the one in Rhizaria)

# so that the IF Phaeosphaeria can map to it

if ott.maybeTaxon('Phaeosphaeria', 'Fungi') == None:

cil = ott.newTaxon('Phaeosphaeria', 'genus', 'if:3951')

cil.setId('5486272')

ott.taxon('Fungi').take(cil)

cil.incertaeSedis()

study713 = taxonomies.load_713()

# ### CHECK: was silva.taxon

ott.addSource(study713)

ott.notSame(study713.taxon('Buchnera', 'Orobanchaceae'), ott.taxon('Buchnera', 'Enterobacteriaceae'))

worms = taxonomies.load_worms()

ott.addSource(worms)

worms.taxon('Viruses').prune("make-ott.py")

# Malacostraca instead of Decapoda because it's in the skeleton

mal = worms.taxon('Malacostraca')

malacostraca = worms.select(mal)

mal.trim()

worms_sans_malacostraca = worms

# Alignment

# https://github.com/OpenTreeOfLife/feedback/issues/45

if False:

ott.same(ott.taxon('Choanoflagellida', 'Opisthokonta'),

worms_sans_malacostraca.taxon('Choanoflagellida'))

ncbi = taxonomies.load_ncbi()

ott.addSource(ncbi)

# 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')

# - Alignment to OTT -

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

# #### Check - was fungi.taxon

# ** No unique taxon found with this name: Burkea

# ** No unique taxon found with this name: Coscinium

# ** No unique taxon found with this name: Perezia

# ott.notSame(ncbi.taxon('Burkea', 'Viridiplantae'), ott.taxon('Burkea'))

# ott.notSame(ncbi.taxon('Coscinium', 'Viridiplantae'), ott.taxon('Coscinium'))

# ott.notSame(ncbi.taxon('Perezia', 'Viridiplantae'), ott.taxon('Perezia'))

# JAR 2014-04-11 Discovered during regression testing

# now handled in other ways

# ott.notSame(ncbi.taxon('Epiphloea', 'Rhodophyta'), ott.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.

# #### Check - was fungi.taxon

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

#ncbi.taxonThatContains('Trichosporon', 'Trichosporon cutaneum')

ncbi.taxon('5552')

)

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

# #### Check - was fungi.taxon

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

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

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

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

# #### Check - was fungi.taxon

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

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

# #### Check - was fungi.taxon

# ott.same(ncbi.taxon('Lamprospora'), ott.taxon('Lamprospora', 'Pyronemataceae'))

# JAR 2014-04-25

# ### CHECK: was silva.taxon

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

# https://github.com/OpenTreeOfLife/feedback/issues/45

if False:

ott.notSame(ott.maybeTaxon('Choanoflagellida', 'Ichthyosporea'),

ncbi.maybeTaxon('Choanoflagellida', 'Opisthokonta'))

# Dail 2014-03-31 https://github.com/OpenTreeOfLife/feedback/issues/5

# updated 2015-06-28 NCBI Katablepharidophyta = SILVA Kathablepharidae.

# ### CHECK: was silva.taxon

ott.same(ncbi.taxon('Katablepharidophyta'), ott.taxon('Kathablepharidae'))

# was: ott.taxon('Katablepharidophyta').hide()

# probably not needed

ott.same(ncbi.taxon('Ciliophora', 'Alveolata'), ott.taxon('Ciliophora', 'Alveolata'))

ott.notSame(ncbi.taxon('Diphylleia', 'Chloroplastida'),

ott.taxonThatContains('Diphylleia', 'Diphylleia rotans'))

# 2015-10-06 JAR noticed while debugging surprisingly large number of newly-hidden ids

# n.b. there are three Ctenophoras: comb jellies, diatom, fly

ott.notSame(ncbi.taxon('Ctenophora', 'Metazoa'),

ott.taxon('Ctenophora', 'Stramenopiles')) # diatom from SILVA, WoRMS, GBIF, IRMNG

infile = open('feed/silva/out/ncbi_to_silva.tsv', 'r')

reader = csv.reader(infile, delimiter='\t')

wins = namings = 0

for (ncbi_id, silva_cluster_id) in reader:

s = silva.maybeTaxon(silva_cluster_id)

if s != None:

n = ncbi.maybeTaxon(ncbi_id)

if n != None:

if False:

so = ott.image(s)

if so != None:

ott.same(n, so)

wins += 1

else:

print '** no OTT taxon for cluster', silva_cluster_id

elif n.name != s.name:

s.setName(n.name)

namings += 1

else:

# 332 occurrences on 2015-10-12

# print '** no NCBI taxon', ncbi_id, 'for cluster', silva_cluster_id

True

else:

print '** no such cluster', silva_cluster_id

if wins > 0:

print wins, 'NCBI ids mapped to clusters'

if namings > 0:

print namings, 'SILVA names updated from more recent NCBI'

gbif = taxonomies.load_gbif()

ott.addSource(gbif)

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

# Fungi suppressed at David Hibbett's request

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

# Suppressed at Laura Katz's request

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

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

# - Alignment -

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

# Automatic alignment makes the wrong choice for this one

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

ott.same(ott.taxon('Ciliophora', 'Alveolata'), gbif.taxon('10')) # in Protozoa

# Not needed?

# ott.same(ott.taxon('Ciliophora', 'Ascomycota'), gbif.taxon('3269382')) # in Fungi

# Automatic alignment makes the wrong choice for this one

# NCBI says ncbi:29178 is in Rhizaria in Eukaryota and contains Allogromida (which is not in GBIF)

# OTT 2.8 has 936399 = in Retaria (which isn't in NCBI) extinct_inherited ? - no good.

# GBIF 389 is in Protozoa... but it contains nothing!! No way to identify it other than by id.

# amoeboid ...

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

# Tetrasphaera is a messy multi-way homonym

#### Check: was ncbi.taxon

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

# Bad alignments to NCBI

# #### THESE NEED TO BE CHECKED - was ncbi.taxon

# Labyrinthomorpha (synonym for Labyrinthulomycetes)

# No longer in GBIF... the one in IRMNG is a Cambrian sponge-like thing

# ott.notSame(ott.taxon('Labyrinthomorpha', 'Stramenopiles'), gbif.taxon('Labyrinthomorpha'))

# ott.notSame(ott.taxon('Ophiurina', 'Echinodermata'), gbif.taxon('Ophiurina','Ophiurinidae'))

# taken care of in taxonomies.py

# There is a test for this. The GBIF taxon no longer exists.

# ott.notSame(ott.taxon('Rhynchonelloidea', 'Brachiopoda'), gbif.taxon('Rhynchonelloidea'))

# There are tests. Seems OK

ott.notSame(ott.taxonThatContains('Neoptera', 'Lepidoptera'), gbif.taxon('Neoptera', 'Diptera'))

# ott.notSame(gbif.taxon('Tipuloidea', 'Chiliocyclidae'), ott.taxon('Tipuloidea', 'Diptera')) # genus Tipuloidea

# taken care of in taxonomies.py

# ### CHECK: was silva.taxon

# SILVA = GN013951 = Tetrasphaera (bacteria)

ott.notSame(ott.taxon('Tetrasphaera', 'Intrasporangiaceae'),

gbif.taxon('Gorkadinium', 'Dinophyta')) # = Tetrasphaera in Protozoa

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

# ### CHECK: was ncbi.taxon

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

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

ott.same(ott.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(fungorum.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'),

# gbif.taxonThatContains('Trichosporon', 'Trichosporon cutaneum'))

# doesn't work. brute force.

# was: ott.same(fungorum.taxon('10296'), gbif.taxon('2518163')) = ott:364222

##### RECOVER THIS IF NECESSARY

# ott.same(fungi.taxon('10296'), ott.taxon('364222'))

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

# if:17806 = Hygrocybe = ott:282216

# #### CHECK: was fungi

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

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

# redundant

# ott.same(gbif.taxon('Lamprospora'), fungi.taxon('Lamprospora'))

# JAR 2014-04-23 IF update fallout

# ### CHECK: was ncbi.taxon

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

ott.taxonThatContains('Penicillium', 'Penicillium expansum'))

# https://github.com/OpenTreeOfLife/feedback/issues/45

# ### CHECK: was ncbi.taxon

if False:

ott.same(gbif.taxon('Choanoflagellida'),

ott.taxon('Choanoflagellida', 'Opisthokonta'))

irmng = taxonomies.load_irmng()

ott.addSource(irmng)

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

# Fungi suppressed at David Hibbett's request

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

# Microbes suppressed at Laura Katz's request

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

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

ott.same(ott.taxon('Veronica', 'Plantaginaceae'), irmng.taxon('1381293')) # ott:648853

# genus Tipuloidea (not superfamily) ott:5708808 = gbif:6101461

# Taken care of in assemble_ott.py:

# ott.same(ott.taxon('Tipuloidea', 'Dicondylia'), irmng.taxon('1170022'))

# IRMNG has four Tetrasphaeras.

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

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

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

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

# Trichosporon in IF = if:10296 genus in Trichosporonaceae

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

# JAR 2014-04-24 false match

# tests pass

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

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

# tests

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

# https://github.com/OpenTreeOfLife/feedback/issues/45

# IRMNG has Choanoflagellida < Zoomastigophora < Sarcomastigophora < Protozoa

# might be better to look for something it contains

ott.same(irmng.taxon('Choanoflagellida', 'Zoomastigophora'),

ott.taxon('Choanoflagellida', 'Eukaryota'))

# probably not needed

ott.same(ott.taxon('Ciliophora', 'Alveolata'), irmng.taxon('239')) # in Protista

# Gone away...

# ott.same(ott.taxon('Ciliophora', 'Ascomycota'), irmng.taxon('Ciliophora', 'Ascomycota'))

# Could force this to not match the arthropod. But much easier just to delete it.

irmng.taxon('Morganella', 'Brachiopoda').prune(this_source)

# ... .notSame(ott.taxon('Morganella', 'Arthropoda'))

# 2015-09-10 Inclusion test failing

ott.notSame(irmng.taxon('Retaria', 'Brachiopoda'), # irmng:1340611

ott.taxon('Retaria', 'Rhizaria'))

# 2015-09-10 Inclusion test failing

ott.notSame(irmng.taxon('Campanella', 'Cnidaria'), # irmng:1289625

ott.taxon('Campanella', 'SAR'))

# 2014-01-27 Joseph: Quiscalus is incorrectly in

# Fringillidae instead of Icteridae. NCBI is wrong, GBIF is correct.

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87

ott.taxon('Icteridae').take(ott.taxon('Quiscalus', 'Fringillidae'))

# Misspelling in GBIF... seems to already be known

# Stephen email to JAR 2014-01-26

# ott.taxon("Torricelliaceae").synonym("Toricelliaceae")

# Joseph 2014-01-27 https://code.google.com/p/gbif-ecat/issues/detail?id=104

ott.taxon('Parulidae').take(ott.taxon('Myiothlypis', 'Passeriformes'))

# I don't get why this one isn't a major_rank_conflict !? - bug. (so to speak.)

ott.taxon('Blattodea').take(ott.taxon('Phyllodromiidae'))

# See above (occurs in both IF and GBIF). Also see issue #67

ott.taxon('Chlamydotomus').incertaeSedis()

# Joseph Brown 2014-01-27

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87

# Occurs as Sakesphorus bernardi in ncbi, gbif, irmng, as Thamnophilus bernardi in bgif

ott.taxon('Thamnophilus bernardi').absorb(ott.taxon('Sakesphorus bernardi'))

ott.taxon('Thamnophilus melanonotus').absorb(ott.taxon('Sakesphorus melanonotus'))

ott.taxon('Thamnophilus melanothorax').absorb(ott.taxon('Sakesphorus melanothorax'))

ott.taxon('Thamnophilus bernardi').synonym('Sakesphorus bernardi')

ott.taxon('Thamnophilus melanonotus').synonym('Sakesphorus melanonotus')

ott.taxon('Thamnophilus melanothorax').synonym('Sakesphorus melanothorax')

# Mammals - groups cluttering basal part of tree

ott.taxon('Litopterna').extinct()

ott.taxon('Notoungulata').extinct()

# Artiodactyls

ott.taxon('Boreameryx').extinct()

ott.taxon('Thandaungia').extinct()

ott.taxon('Limeryx').extinct()

ott.taxon('Delahomeryx').extinct()

ott.taxon('Krabitherium').extinct()

ott.taxon('Discritochoerus').extinct()

ott.taxon('Brachyhyops').extinct()

# Not fungi - Romina 2014-01-28

# ott.taxon('Adlerocystis').show() - it's Chromista ...

# Index Fungorum says Adlerocystis is Chromista, but I don't believe it

# ott.taxon('Chromista').take(ott.taxon('Adlerocystis','Fungi'))

# Adlerocystis seems to be a fungus, but unclassified - JAR 2014-03-10

ott.taxon('Adlerocystis').incertaeSedis()

# "No clear identity has emerged"

# http://forestis.rsvs.ulaval.ca/REFERENCES_X/phylogeny.arizona.edu/tree/eukaryotes/accessory/parasitic.html

# Need to hide it because it clutters base of Fungi

if ott.maybeTaxon('Amylophagus','Fungi') != None:

ott.taxon('Amylophagus','Fungi').incertaeSedis()

# Bad synonym - Tony Rees 2014-01-28

# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/ihooRUSayXkJ

if ott.maybeTaxon('Lemania pluvialis') != None:

ott.taxon('Lemania pluvialis').prune("make-ott.py")

# Tony Rees 2014-01-29

# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/wTeD17GzOGoJ

trigo = ott.maybeTaxon('Trigonocarpales')

if trigo != None: trigo.extinct()

#Pinophyta and daughters need to be deleted; - Bryan 2014-01-28

#Lycopsida and daughters need to be deleted;

#Pteridophyta and daughters need to be deleted;

#Gymnospermophyta and daughters need to be deleted;

for name in ['Pinophyta', 'Pteridophyta', 'Gymnospermophyta']:

if ott.maybeTaxon(name,'Chloroplastida'):

ott.taxon(name,'Chloroplastida').incertaeSedis()

# Patches from the Katz lab to give decent parents to taxa classified

# as Chromista or Protozoa

print '-- Chromista/Protozoa spreadsheet from Katz lab --'

fixChromista(ott)

print '-- more patches --'

# From Laura and Dail on 5 Feb 2014

# https://groups.google.com/d/msg/opentreeoflife/a69fdC-N6pY/y9QLqdqACawJ

tax = ott.maybeTaxon('Chlamydiae/Verrucomicrobia group')

if tax != None and tax.name != 'Bacteria':

tax.rename('Verrucomicrobia group')

ott.taxon('Heterolobosea','Discicristata').absorb(ott.taxon('Heterolobosea','Percolozoa'))

ott.taxon('Excavata','Eukaryota').take(ott.taxon('Oxymonadida','Eukaryota'))

# There is no Reptilia in OTT 2.9, so this can probably be deleted

if ott.maybeTaxon('Reptilia') != None:

ott.taxon('Reptilia').hide()

# Chris Owen patches 2014-01-30

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/88

ott.taxon('Protostomia').take(ott.taxon('Chaetognatha','Deuterostomia'))

ott.taxon('Lophotrochozoa').take(ott.taxon('Platyhelminthes'))

ott.taxon('Polychaeta','Annelida').take(ott.taxon('Myzostomida'))

ott.taxon('Lophotrochozoa').take(ott.taxon('Gnathostomulida'))

# https://dx.doi.org/10.1007/s13127-011-0044-4

# Not in deuterostomes

ott.taxon('Bilateria').take(ott.taxon('Xenacoelomorpha'))

# 8) Stauromedusae should be a class (Staurozoa; Marques and Collins 2004) and should be removed from Scyphozoa

ott.taxon('Cnidaria').take(ott.taxon('Stauromedusae'))

ott.taxon('Copepoda').take(ott.taxon('Prionodiaptomus'))

# Bryan Drew patches 2014-01-30

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/89

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90

ott.taxon('Scapaniaceae').absorb(ott.taxon('Lophoziaceae'))

ott.taxon('Salazaria mexicana').rename('Scutellaria mexicana')

# One Scutellaria is in Lamiaceae; the other is a fungus.

# IRMNG's Salazaria 1288740 is in Lamiales, and is a synonym of Scutellaria.

##### RECOVER THIS SOMEHOW --

# ott.taxon('Scutellaria','Lamiaceae').absorb(ott.image(gbif.taxon('Salazaria')))

# IRMNG 1288740 not in newer IRMNG

if False:

sal = irmng.maybeTaxon('1288740')

if sal != None:

ott.taxon('Scutellaria','Lamiaceae').absorb(ott.image(sal)) #Salazaria

# Make an order Boraginales that contains Boraginaceae + Hydrophyllaceae

# http://dx.doi.org/10.1111/cla.12061

# Bryan Drew 2013-09-30

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/91

ott.taxon('Boraginaceae').absorb(ott.taxon('Hydrophyllaceae'))

ott.taxon('Boraginales').take(ott.taxon('Boraginaceae'))

ott.taxon('lamiids').take(ott.taxon('Boraginales'))

# Bryan Drew 2014-01-30

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90

# Vahlia 26024 <- Vahliaceae 23372 <- lammids 596112 (was incertae sedis)

ott.taxon('lamiids').take(ott.taxon('Vahliaceae'))

# Bryan Drew 2014-01-30

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90

# http://www.sciencedirect.com/science/article/pii/S0034666703000927

ott.taxon('Araripia').extinct()

# Bryan Drew 2014-02-05

# http://www.mobot.org/mobot/research/apweb/

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/92

ott.taxon('Viscaceae').rename('Visceae')

ott.taxon('Amphorogynaceae').rename('Amphorogyneae')

ott.taxon('Thesiaceae').rename('Thesieae')

ott.taxon('Santalaceae').take(ott.taxon('Visceae'))

ott.taxon('Santalaceae').take(ott.taxon('Amphorogyneae'))

ott.taxon('Santalaceae').take(ott.taxon('Thesieae'))

ott.taxon('Santalaceae').absorb(ott.taxon('Cervantesiaceae'))

ott.taxon('Santalaceae').absorb(ott.taxon('Comandraceae'))

# Bryan Drew 2014-01-30

# http://dx.doi.org/10.1126/science.282.5394.1692

ott.taxon('Magnoliophyta').take(ott.taxon('Archaefructus'))

# Bryan Drew 2014-01-30

# http://deepblue.lib.umich.edu/bitstream/handle/2027.42/48219/ID058.pdf

ott.taxon('eudicotyledons').take(ott.taxon('Phyllites'))

# Bryan Drew 2014-02-13

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/93

# http://dx.doi.org/10.1007/978-3-540-31051-8_2

ott.taxon('Alseuosmiaceae').take(ott.taxon('Platyspermation'))

# JAR 2014-02-24. We are getting extinctness information for genus

# and above from IRMNG, but not for species.

# There's a similar problem in Equus.

for name in ['Homo sapiens neanderthalensis',

'Homo sapiens ssp. Denisova',

'Homo habilis',

'Homo erectus',

'Homo cepranensis',

'Homo georgicus',

'Homo floresiensis',

'Homo kenyaensis',

'Homo rudolfensis',

'Homo antecessor',

'Homo ergaster',

'Homo okotensis']:

tax = ott.maybeTaxon(name)

if tax != None:

tax.extinct()

# JAR 2014-03-07 hack to prevent H.s. from being extinct due to all of

# its subspecies being extinct.

# I wish I knew what the authority for the H.s.s. name was.

hss = ott.newTaxon('Homo sapiens sapiens', 'subspecies', 'https://en.wikipedia.org/wiki/Homo_sapiens_sapiens')

ott.taxon('Homo sapiens').take(hss)

hss.hide()

# Raised by Joseph Brown 2014-03-09, solution proposed by JAR

# Tribolium is incertae sedis in NCBI but we want it to not be hidden,

# since it's a model organism.

# Placement in Tenebrioninae is according to http://bugguide.net/node/view/152 .

# Is this cheating?

ott.taxon('Tenebrioninae').take(ott.taxon('Tribolium','Coleoptera'))

# Bryan Drew 2014-03-20 http://dx.doi.org/10.1186/1471-2148-14-23

ott.taxon('Pentapetalae').take(ott.taxon('Vitales'))

# Bryan Drew 2014-03-14 http://dx.doi.org/10.1186/1471-2148-14-23

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/24

ott.taxon('Streptophytina').elide()

# Dail 2014-03-20

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/29

# Note misspelling in SILVA

ott.taxon('Freshwayer Opisthokonta').rename('Freshwater Microbial Opisthokonta')

# JAR 2014-03-31 just poking around

# Many of these would be handled by major_rank_conflict if it worked

for name in [

'Temnospondyli', # http://tolweb.org/tree?group=Temnospondyli

'Eobatrachus', # https://en.wikipedia.org/wiki/Eobatrachus

'Vulcanobatrachus', # https://en.wikipedia.org/wiki/Vulcanobatrachus

'Beelzebufo', # https://en.wikipedia.org/wiki/Beelzebufo

'Iridotriton', # https://en.wikipedia.org/wiki/Iridotriton

'Baurubatrachus', # https://en.wikipedia.org/wiki/Baurubatrachus

'Acritarcha', # # JAR 2014-04-26

]:

tax = ott.maybeTaxon(name)

if tax != None: tax.extinct()

# Dail 2014-03-31 https://github.com/OpenTreeOfLife/feedback/issues/4

# no evidence given

ott.taxonThatContains('Bacteria', 'Lentisphaerae').take(ott.taxon('Lentisphaerae'))

# David Hibbett 2014-04-02 misspelling in h2007 file

# (Dacrymecetales is 'no rank', Dacrymycetes is a class)

if ott.maybeTaxon('Dacrymecetales') != None:

ott.taxon('Dacrymecetales').rename('Dacrymycetes')

# Dail https://github.com/OpenTreeOfLife/feedback/issues/6

ott.taxon('Telonema').synonym('Teleonema')

# Joseph https://github.com/OpenTreeOfLife/reference-taxonomy/issues/43

ott.taxon('Lorisiformes').take(ott.taxon('Lorisidae'))

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

# As of 2014-04-23 IF synonymizes Cyphellopsis to Merismodes

cyph = ott.maybeTaxon('Cyphellopsis','Cyphellaceae')

if cyph != None:

cyph.unhide()

if ott.maybeTaxon('Cyphellopsis','Niaceae') != None:

cyph.absorb(ott.taxon('Cyphellopsis','Niaceae'))

ott.taxon('Diaporthaceae').take(ott.taxon('Phomopsis'))

ott.taxon('Valsaceae').take(ott.taxon('Valsa', 'Fungi'))

ott.taxon('Agaricaceae').take(ott.taxon('Cystoderma','Fungi'))

# Invert the synonym relationship

ott.taxon('Hypocrea lutea').absorb(ott.taxon('Trichoderma deliquescens'))

# Fold Norops into Anolis

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/31

# TBD: Change species names from Norops X to Anolis X for all X

ott.taxon('Anolis').absorb(ott.maybeTaxon('Norops', 'Iguanidae'))

for (name, super) in [

# JAR 2014-04-08 - these are in study OTUs - see IRMNG

('Inseliellum', None),

('Conus', 'Gastropoda'),

('Patelloida', None),

('Phyllanthus', 'Phyllanthaceae'),

('Stelis','Orchidaceae'),

('Chloris', 'Poaceae'),

('Acropora', 'Acroporidae'),

('Diadasia', None),

# JAR 2014-04-24

# grep "ncbi:.*extinct_inherited" tax/ott/taxonomy.tsv | head

('Tarsius', None),

('Odontesthes', None),

('Leiognathus', 'Chordata'),

('Oscheius', None),

('Cicindela', None),

('Leucothoe', 'Ericales'),

('Hydrornis', None),

('Bostrychia harveyi', None), #fungus

('Agaricia', None), #coral

('Dischidia', None), #eudicot

# JAR 2014-05-13

('Saurischia', None),

# there are two of these, maybe should be merged.

# 'Myoxidae', 'Rodentia'),

# JAR 2014-05-13 These are marked extinct by IRMNG but are all in NCBI

# and have necleotide sequences

('Zemetallina', None),

('Nullibrotheas', None),

('Fissiphallius', None),

('Nullibrotheas', None),

('Sinelater', None),

('Phanerothecium', None),

('Cephalotaxaceae', None),

('Vittaria elongata', None),

('Neogymnocrinus', None),

]:

if super == None:

tax = ott.maybeTaxon(name)

else:

tax = ott.maybeTaxon(name, super)

if tax != None: tax.extant()

# JAR 2014-05-08 while looking at the deprecated ids file.

# http://www.theplantlist.org/tpl/record/kew-2674785

ott.taxon('Berendtiella rugosa').synonym('Berendtia rugosa')

# JAR 2014-05-13 weird problem

# NCBI incorrectly has both Cycadidae and Cycadophyta as children of Acrogymnospermae.

# Cycadophyta (class, with daughter Cycadopsida) has no sequences.

# The net effect is a bunch of extinct IRMNG genera showing up in

# Cycadophyta, with Cycadophyta entirely extinct.

#

# NCBI has subclass Cycadidae = order Cycadales

# GBIF has phylum Cycadophyta = class Cycadopsida = order Cycadales

# IRMNG has class Cycadopsida = order Cycadales

if ott.maybeTaxon('Cycadidae') != None:

ott.taxon('Cycadidae').absorb(ott.taxon('Cycadopsida'))

ott.taxon('Cycadidae').absorb(ott.taxon('Cycadophyta'))

# Similar problem with Gnetidae and Ginkgoidae

# Dail 2014-03-31

# https://github.com/OpenTreeOfLife/feedback/issues/6

ott.taxon('Telonema').synonym('Teleonema')

# JAR noticed 2015-02-17 used in pg_2460

# http://reptile-database.reptarium.cz/species?genus=Parasuta&species=spectabilis

ott.taxon('Parasuta spectabilis').synonym('Rhinoplocephalus spectabilis')

# Bryan Drew 2015-02-17 http://dx.doi.org/10.1016/j.ympev.2014.11.011

sax = ott.taxon('Saxifragella bicuspidata')

ott.taxon('Saxifraga').take(sax)

sax.rename('Saxifraga bicuspidata')

# JAR 2015-07-21 noticed, obviously wrong

ott.taxonThatContains('Ophiurina', 'Acrocnida brachiata').extant()

# straightening out an awful mess

ott.taxon('Saccharomycetes', 'Saccharomycotina').extant() # foo. don't know who sets this

ott.taxonThatContains('Rhynchonelloidea', 'Sphenarina').extant() # NCBI

# "Old" patch system

ott.edit('feed/ott/edits/')

# This is a randomly chosen bivalve to force Bivalvia to not be extinct

ott.taxon('Corculum cardissa', 'Bivalvia').extant()

# Similarly for roaches

infile = open('tax/gbif/paleo.tsv')

paleos = 0

flagged = 0

for row in infile:

paleos += 1

id = row.strip()

gtaxon = gbif.lookupId(id)

if gtaxon != None:

taxon = ott.image(gtaxon)

if taxon != None:

if len(taxon.sourceIds) == 1:

flagged += 1

taxon.extinct()

infile.close()

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/68

# 'Extinct' would really mean 'extinct and no sequence' with this change

print 'Non-extincting NCBI'

def recur(node):

unode = ott.image(node)

if node.children == None:

if unode == None:

return True

else:

return unode.isAnnotatedExtinct()

else:

inct = True

for child in node.children:

inct = inct and recur(child)

if not inct:

if unode != None and unode.isAnnotatedExtinct():

# Contains a possibly extant descendant...

print 'Changing from extinct to extant', unode.name, unode.id

unode.extant()

return False

else:

return True

for node in ncbi.roots():

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

print '-- Checking realization of h2007'

for taxon in h2007:

im = ott.image(taxon)

if im != None:

if im.children == None:

print '** Barren taxon from h2007', taxon.name

else:

print '-- Parent/child homonyms'

ott.parentChildHomonymReport()