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Added values to synonyms table #383

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Added values to synonyms table #383

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59 changes: 39 additions & 20 deletions ete3/ncbi_taxonomy/ncbiquery.py
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@ def get_lineage_translator(self, taxids):

return id2lineages


def get_lineage(self, taxid):
"""Given a valid taxid number, return its corresponding lineage track as a
hierarchically sorted list of parent taxids.
Expand All @@ -241,7 +241,7 @@ def get_lineage(self, taxid):
raise ValueError("%s taxid not found" %taxid)
else:
warnings.warn("taxid %s was translated into %s" %(taxid, merged_conversion[taxid]))

track = list(map(int, raw_track[0].split(",")))
return list(reversed(track))

Expand All @@ -255,6 +255,25 @@ def get_common_names(self, taxids):
id2name[tax] = common_name
return id2name

def get_synonyms(self, taxids):
"""
Given a list of taxids, returns a dictionary with their corresponding
synonyms.
"""
id2syn = {}
# since they could be more than one synonym
# we first create a dictionary filled with taxonID
# and have an array of values/synonyms
for tax in taxids:
id2syn[tax] = []
query = ','.join(['"%s"' %v for v in taxids])
cmd = "select taxid, spname FROM synonym WHERE taxid IN (%s);" %query
result = self.db.execute(cmd)
for tax, synonym in result.fetchall():
if synonym:
id2syn[tax].append(synonym)
return id2syn

def get_taxid_translator(self, taxids, try_synonyms=True):
"""Given a list of taxids, returns a dictionary with their corresponding
scientific names.
Expand Down Expand Up @@ -326,7 +345,7 @@ def translate_to_names(self, taxids):
for sp in taxids:
names.append(id2name.get(sp, sp))
return names


def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False):
"""
Expand All @@ -353,12 +372,12 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
descendants[tid] = descendants.get(tid, 0) + 1
elif found == 2:
break

if not found:
raise ValueError("taxid not found:%s" %taxid)
elif found == 1:
return [taxid]
return [taxid]

if rank_limit or collapse_subspecies or return_tree:
tree = self.get_topology(list(descendants.keys()), intermediate_nodes=intermediate_nodes, collapse_subspecies=collapse_subspecies, rank_limit=rank_limit)
if return_tree:
Expand All @@ -367,7 +386,7 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
return list(map(int, [n.name for n in tree.get_descendants()]))
else:
return map(int, [n.name for n in tree])

elif intermediate_nodes:
return [tid for tid, count in six.iteritems(descendants)]
else:
Expand All @@ -393,7 +412,7 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap

"""
from .. import PhyloTree
taxids, merged_conversion = self._translate_merged(taxids)
taxids, merged_conversion = self._translate_merged(taxids)
if len(taxids) == 1:
root_taxid = int(list(taxids)[0])
with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
Expand All @@ -402,14 +421,14 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap
found = 0
nodes = {}
hit = 0
visited = set()
visited = set()
start = prepostorder.index(root_taxid)
try:
end = prepostorder.index(root_taxid, start+1)
subtree = prepostorder[start:end+1]
end = prepostorder.index(root_taxid, start+1)
subtree = prepostorder[start:end+1]
except ValueError:
# If root taxid is not found in postorder, must be a tip node
subtree = [root_taxid]
subtree = [root_taxid]
leaves = set([v for v, count in Counter(subtree).items() if count == 1])
nodes[root_taxid] = PhyloTree(name=str(root_taxid))
current_parent = nodes[root_taxid]
Expand All @@ -430,7 +449,7 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap
id2lineage = self.get_lineage_translator(taxids)
all_taxids = set()
for lineage in id2lineage.values():
all_taxids.update(lineage)
all_taxids.update(lineage)
id2rank = self.get_rank(all_taxids)
for sp in taxids:
track = []
Expand Down Expand Up @@ -488,7 +507,7 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax

:param t: a Tree (or Tree derived) instance.

:param name taxid_attr: Allows to set a custom node attribute
:param name taxid_attr: Allows to set a custom node attribute
containing the taxid number associated to each node (i.e.
species in PhyloTree instances).

Expand All @@ -508,7 +527,7 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
merged_conversion = {}

taxids, merged_conversion = self._translate_merged(taxids)

if not tax2name or taxids - set(map(int, list(tax2name.keys()))):
tax2name = self.get_taxid_translator(taxids)
if not tax2track or taxids - set(map(int, list(tax2track.keys()))):
Expand Down Expand Up @@ -538,7 +557,7 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
n.add_features(sci_name = tax2name.get(node_taxid, getattr(n, taxid_attr, '')),
common_name = tax2common_name.get(node_taxid, ''),
lineage = tax2track[node_taxid],
rank = tax2rank.get(node_taxid, 'Unknown'),
rank = tax2rank.get(node_taxid, 'Unknown'),
named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track[node_taxid]])
elif n.is_leaf():
n.add_features(sci_name = getattr(n, taxid_attr, 'NA'),
Expand Down Expand Up @@ -680,7 +699,8 @@ def load_ncbi_tree_from_dump(tar):
if name_type == "genbank common name":
node2common[nodename] = taxname
elif name_type in set(["synonym", "equivalent name", "genbank equivalent name",
"anamorph", "genbank synonym", "genbank anamorph", "teleomorph"]):
"anamorph", "genbank synonym", "genbank anamorph", "teleomorph",
"common name", "authority"]):
synonyms.add( (nodename, taxname) )
print(len(node2taxname), "names loaded.")
print(len(synonyms), "synonyms loaded.")
Expand Down Expand Up @@ -744,7 +764,7 @@ def update_db(dbfile, targz_file=None):
md5_check = md5_file.readline().split()[0]
targz_file = "taxdump.tar.gz"
do_download = False

if os.path.exists("taxdump.tar.gz"):
local_md5 = md5(open("taxdump.tar.gz", "rb").read()).hexdigest()
if local_md5 != md5_check:
Expand Down Expand Up @@ -778,7 +798,7 @@ def update_db(dbfile, targz_file=None):
raise
else:
os.system("rm syn.tab merged.tab taxa.tab")
# remove only downloaded taxdump file
# remove only downloaded taxdump file
if not targz_file:
os.system("rm taxdump.tar.gz")

Expand Down Expand Up @@ -847,4 +867,3 @@ def upload_data(dbfile):

print(ncbi.get_common_names(b))
#ncbi.update_taxonomy_database()