def doSilva():
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)
return silva
def doSilva():
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)
return silva
# Requires python.security.respectJavaAccessibility = false
# on java command line or in .jython
from org.opentreeoflife.taxa import Taxonomy
from org.opentreeoflife.smasher import UnionTaxonomy, HomonymReport
union = UnionTaxonomy()
skel = Taxonomy.getTaxonomy('tax/skel/', 'skel')
union.setSkeleton(skel)
def report(tax, tag):
union.markDivisionsFromSkeleton(tax, skel)
HomonymReport.homonymReport(tax, 'reports/' + tag + '-homonym-report.tsv')
if True:
ott = Taxonomy.getTaxonomy('tax/ott/', 'ott')
report(ott, 'ott')
else:
import taxonomies
report(taxonomies.loadSilva(), 'silva')
report(taxonomies.loadH2007(), 'h2007')
report(taxonomies.loadFung(), 'worms')
report(taxonomies.loadFung(), 'if')
report(taxonomies.loadNcbi(), 'ncbi')
report(taxonomies.loadGbif(), 'gbif')
report(taxonomies.loadIrmng(), 'irmng')
from org.opentreeoflife.smasher import Taxonomy
from org.opentreeoflife.smasher import Reportx
import taxonomies
ott = Taxonomy.newTaxonomy()
skel = Taxonomy.getTaxonomy('tax/skel/', 'skel')
ott.setSkeleton(skel)
def report(tax, tag):
ott.markDivisions(tax)
# Reportx.bogotypes(tax)
taxonomies.checkDivisions(tax)
Reportx.report(tax, tag + '-mrca-report.tsv')
if True:
report(taxonomies.loadIrmng(), 'irmng')
else:
silva = taxonomies.loadSilva()
ott.notSame(silva.taxon('Ctenophora', 'Coscinodiscophytina'),
skel.taxon('Ctenophora'))
report(silva, 'silva')
report(taxonomies.loadH2007(), 'h2007')
report(taxonomies.loadFung(), 'if')
report(taxonomies.loadNcbi(), 'ncbi')
report(taxonomies.loadGbif(), 'gbif')
report(taxonomies.loadIrmng(), 'irmng')
report(taxonomies.loadOtt(), 'ott')
# Requires python.security.respectJavaAccessibility = false
# on java command line or in .jython
from org.opentreeoflife.taxa import Taxonomy
from org.opentreeoflife.smasher import UnionTaxonomy, HomonymReport
union = UnionTaxonomy()
skel = Taxonomy.getTaxonomy('tax/skel/', 'skel')
union.setSkeleton(skel)
def report(tax, tag):
union.markDivisionsFromSkeleton(tax, skel)
HomonymReport.homonymReport(tax, 'reports/' + tag + '-homonym-report.tsv')
if True:
ott = Taxonomy.getTaxonomy('tax/ott/', 'ott')
report(ott, 'ott')
else:
import taxonomies
report(taxonomies.loadSilva(), 'silva')
report(taxonomies.loadH2007(), 'h2007')
report(taxonomies.loadFung(), 'worms')
report(taxonomies.loadFung(), 'if')
report(taxonomies.loadNcbi(), 'ncbi')
report(taxonomies.loadGbif(), 'gbif')
report(taxonomies.loadIrmng(), 'irmng')
from org.opentreeoflife.smasher import Taxonomy
from org.opentreeoflife.smasher import Reportx
import taxonomies
ott = Taxonomy.newTaxonomy()
skel = Taxonomy.getTaxonomy('tax/skel/', 'skel')
ott.setSkeleton(skel)
def report(tax, tag):
ott.markDivisions(tax)
# Reportx.bogotypes(tax)
taxonomies.checkDivisions(tax)
Reportx.report(tax, tag + '-mrca-report.tsv')
if True:
report(taxonomies.loadIrmng(), 'irmng')
else:
silva = taxonomies.loadSilva()
ott.notSame(silva.taxon('Ctenophora', 'Coscinodiscophytina'),
skel.taxon('Ctenophora'))
report(silva, 'silva')
report(taxonomies.loadH2007(), 'h2007')
report(taxonomies.loadFung(), 'if')
report(taxonomies.loadNcbi(), 'ncbi')
report(taxonomies.loadGbif(), 'gbif')
report(taxonomies.loadIrmng(), 'irmng')
report(taxonomies.loadOtt(), 'ott')