# One-off script prepared to provide data to David Hibbett and Romina Gazis.
# Lists numbers of species in each fungal order.
from org.opentreeoflife.taxa import Taxonomy
import csv, sys
from taxonomies import load_fung, load_ncbi, load_gbif, load_irmng
taxonomies = [('fung', load_fung(), 'Index Fungorum'),
('ncbi', load_ncbi(), 'NCBI'),
('gbif', load_gbif(), 'GBIF'),
('irmng', load_irmng(), 'IRMNG'),
('ott', Taxonomy.getTaxonomy('tax/ott/'), 'OTT 2.9'),
]
def main():
infile = open('order-counts-orders.csv', 'r')
reader = csv.reader(infile)
reader.next() #header row
taxa = ['Fungi']
for tuple in reader:
taxa.append(tuple[0])
infile.close()
write_counts(taxa)
def write_counts(taxa):
outfile = open('order-counts.csv', 'w')
writer = csv.writer(outfile)
header = ['order']
for (name, taxonomy, label) in taxonomies:
header += [label + ' bin', label + ' sp', label + ' tip']
# One-off script prepared to provide data to David Hibbett and Romina Gazis.
# Lists numbers of species in each fungal order.
from org.opentreeoflife.smasher import Taxonomy
import csv, sys
from taxonomies import load_fung, load_ncbi, load_gbif, load_irmng
taxonomies = [
("fung", load_fung(), "Index Fungorum"),
("ncbi", load_ncbi(), "NCBI"),
("gbif", load_gbif(), "GBIF"),
("irmng", load_irmng(), "IRMNG"),
("ott", Taxonomy.getTaxonomy("tax/ott/"), "OTT 2.9"),
]
def main():
infile = open("order-counts-orders.csv", "r")
reader = csv.reader(infile)
reader.next() # header row
taxa = ["Fungi"]
for tuple in reader:
taxa.append(tuple[0])
infile.close()
write_counts(taxa)
def write_counts(taxa):
outfile = open("order-counts.csv", "w")
writer = csv.writer(outfile)
# One-off script prepared to provide data to David Hibbett and Romina Gazis.
# Lists numbers of species in each fungal order.
from org.opentreeoflife.smasher import Taxonomy
import csv, sys
from taxonomies import load_fung, load_ncbi, load_gbif, load_irmng
taxonomies = [
('fung', load_fung(), 'Index Fungorum'),
('ncbi', load_ncbi(), 'NCBI'),
('gbif', load_gbif(), 'GBIF'),
('irmng', load_irmng(), 'IRMNG'),
('ott', Taxonomy.getTaxonomy('tax/ott/'), 'OTT 2.9'),
]
def main():
infile = open('order-counts-orders.csv', 'r')
reader = csv.reader(infile)
reader.next() #header row
taxa = ['Fungi']
for tuple in reader:
taxa.append(tuple[0])
infile.close()
write_counts(taxa)
def write_counts(taxa):
outfile = open('order-counts.csv', 'w')
writer = csv.writer(outfile)
def prepare_fungorum(ott):
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()
return (fungi, fungorum)
def prepare_fungorum(ott):
fungorum = taxonomies.load_fung()
fungorum.setTarget(ott)
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()
return (fungi, fungorum)