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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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