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"""
This process the tree from the Hug et al 2016 paper into a genus-resolved tree
with NCBI tax ids for the leafs. This helps make it a little more amenable to
graphing (i.e. shorter labels and fewer of them) and comparing with the
preexisting NCBI taxonomy.
(Note that not all of the nodes can be resolved into tax ids using this name
matching and the current NCBI taxonomy (e.g. CPR phyla don't generally have
genus resolution yet). Also, I had to drop some members of some of the genuses
to ensure no genuses were paraphyletic. This is good enough for my purposes, but
if you're dealing with new organisms or need more accurate resolution of the
true position of e.g. Clostridium, etc you may need to try something different.
The final Newick tree is the last line of the file for ease of copying. To run
you will need the tree itself (Supplementary Dataset 2; saved as hug.nwk) from:
http://www.nature.com/articles/nmicrobiol201648
You also need an uncompressed copy of taxdump.tar.gz from:
ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/
"""
from collections import Counter
from skbio import TreeNode
blocked = (
# drop species with draft/unfinished genomes that cause paraphyletic splits
'Eubacterium cylindroides T2 87 draft genome.',
'Lyngbya sp. PCC 8106 unfinished sequence',
'Peptostreptococcus micros ATCC 33270 unfinished sequence',
'Oceanobacter sp. RED65 unfinished sequence',
'Bacteroides pectinophilus ATCC 43243 unfinished sequence',
'Clostridium nexile DSM 1787 unfinished sequence',
'Eubacterium biforme DSM 3989 unfinished sequence',
# drop other genomes which cause paraphyletic splits and appear to be
# grouping with things outside their NCBI taxonomy
'Lactobacillus acidophilus NCFM',
'Pseudomonas flectens ATCC 12775',
'Streptococcus pleomorphus DSM 20574',
'Cytophagaceae Cytophaga fermentans IAM 14302 DSM 9555',
'Curtobacterium ginsengisoli DSM 22003',
'Nitrospira uncultured SMTZ 35',
'Candidatus Nitrospira defluvii',
'Halorubrum sp. A07HR60',
'Bacillus tusciae DSM 2912',
'Thermodesulfovibrio yellowstonii DSM 11347',
'Spirochaete 67 19',
'Ruminococcus obeum A2 162 draft genome.',
# delete things which are closely related, /-A1
# but form a small outgroup because another --| /-A2
# strain is interspersed (e.g. A1 to the right) \--/--B
'Geobacillus debilis gb1 GenePRIMP',
'Marinilabiaceae Anaerophaga sp. HS1',
'Haliea salexigens DSM 19537',
'Vibrio fischeri MJ11 I',
'Frateuria aurantia Kondo 67 DSM 6220',
'Aurantimonadaceae Aurantimonas ureilytica DSM 18598',
'Prevotella tannerae ATCC 51259',
'Acidobacterium capsulatum ATCC 51196',
'Thermoproteus uzoniensis 768 20 chromosome',
'Microcoleus sp. PCC 7113',
# drop other genomes (i'm not thrilled with these choices and
# don't have strong evidence they're the best, but they're needed to
# make every genus make uniquely)
'Cyanobacterium stanieri PCC 7202',
'Synechocystis sp. PCC 6308',
'Bdellovibrionales 49 15',
'Bdellovibrionales 40 8',
'Bdellovibrio bacteriovorus HD100',
'AWQC131C Submitted file with automatic translation by Kostas',
'Thalassiobium sp. R2A62 genomic scaffold scf 1112329232034',
'Desulfobacterium anilini DSM 4660',
'Mannheimia succiniciproducens MBEL55E',
'Nostoc sp. PCC 7524',
'Pichia pastoris GS115',
'Pichia guilliermondii ATCC 6260',
'Eubacterium sp. AS15',
'Kluyveromyces lactis NRRL Y 1140',
'Candida dubliniensis CD36',
'Alteromonas macleodii Black Sea 11',
'Bacillus anthracis 52 G',
'Bacillus gelatini DSM 15865',
'Clostridium innocuum 2959',
'Clostridium phytofermentans ISDg',
'Clostridium lentocellum DSM 5427',
'Clostridium orbiscindens 1 3 50AFAA',
'Clostridium clariflavum EBR 45 DSM 19732',
'Clostridium acidurici 9a DSM 604',
'Clostridium acetobutylicum EA 2018',
)
# get every genus in NCBI's tax_id
genus_ids = set()
for line in open('taxdmp/nodes.dmp', 'r'):
fields = line.split('\t|\t')
if fields[2] == 'genus':
genus_ids.add(fields[0])
# make a quick name -> tax id lookup table using the list of known genuses
name_to_id = {}
for line in open('taxdmp/names.dmp', 'r'):
fields = line.split('\t|\t')
if fields[0] in genus_ids:
name_to_id[fields[1]] = fields[0]
# scan the names again, picking up anything that is both a genus name and the
# name of some other taxonomic level (e.g. bacteria)
# Deinococcus and Thermus seem to fall in this category, but aren't reflected
# in NCBI (yet)
trouble_genuses = {'Deinococcus', 'Thermus', 'Bdellovibrio'}
for line in open('taxdmp/names.dmp', 'r'):
fields = line.split('\t|\t')
if fields[0] not in genus_ids and fields[1] in name_to_id:
trouble_genuses.add(fields[1])
n_ident = 0
hug_tree = TreeNode.read(open('hug.nwk', 'r'))
for tip in hug_tree.tips():
name = tip.name
assert name.startswith(('Archaea', 'Bacteria',
'Eukaryota', 'Archaeplastida'))
# merge the word "group" into the previous word to handle the edge
# case of species groups that have a genus name too (e.g. Chromobacterium
# group, Moorella group)
name = name.replace(' group', 'group')
# figure out all the possible genuses this could belong to; always
# block Bacteria because we don't think there are any stick insects in here
# and this *will* match if the true genus isn't in NCBI
genuses = []
for word in name.split():
if word in name_to_id and word not in ['Bacteria']:
genuses.append(word)
# if there are multiple (conflicting) genuses, strip off any known
# "problematic" genuses from the beginning (e.g. Bacteria) -> this leaves
# the good genus followed (in rare cases) by another genus that this species
# is a host on
if len(set(genuses)) > 1:
while True:
if genuses[0] in trouble_genuses and len(genuses) > 1:
genuses.pop(0)
else:
break
# filtering out "unfinished" genomes removes e.g.
# "Bacteroides pectinophilus ATCC 43243 unfinished sequence"
# which clusters with the Firmicutes instead of the Bacteroidetes
if len(genuses) == 0 or name.endswith(blocked):
# if there's no possible genus, add it to a list to remove later
tip.name = None
else:
# otherwise update the name to the tax_id
tip.name = name_to_id[genuses[0]]
n_ident += 1
# do a pre-order traversal of the tree, checking the nodes at every time
# if all tips are null, delete the parent (prune off any unclassified branches)
for node in hug_tree.preorder():
names = set(t.name for t in node.tips())
if names == {None} or (node.is_tip() and node.name is None):
# delete me and all my children
node.parent.remove(node)
hug_tree.prune()
# redo the traversal, and if all the tips have the same genus,
# update the parent to have that genus (roll up the genuses/genii/whatever)
for node in hug_tree.preorder():
names = set(t.name for t in node.tips())
if len(names) == 1:
# all my children have the same name so change my name to my that
# and delete all my children
node.name = list(names)[0]
node.children = []
# a quick check to make sure nothing is paraphyletic and each genus is present
# only once
genus_count = Counter([t.name for t in hug_tree.tips()])
paraphyletic = [t for t, n in genus_count.items() if n > 1]
assert len(paraphyletic) == 0
hug_tree.write(open('new_hug.nwk', 'w'))
# the final output should be:
assert """
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"""
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