def prepare_irmng(ott):
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'))
return irmng
# 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)
def prepare_irmng(ott):
irmng = taxonomies.load_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'))
return irmng
