# 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']
def prepare_gbif(ott):
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'))
return gbif
# 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_gbif(ott):
gbif = taxonomies.load_gbif()
gbif.setTarget(ott)
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'))
return gbif