def genNamesDict(resolver, logger, parentid=None):
"""Return a dictionary containing all names and metadata"""
# extract lists from resolver
qnames = resolver.retrieve('query_name')
qnames = [re.sub("\s", "_", e) for e in qnames] # no spaces
ranks = resolver.retrieve('classification_path_ranks')
# in order to get name, ID and rank for the context let's use a zipped
# lineage IDs
lids = resolver.retrieve('classification_path_ids')
lineages = zip(resolver.retrieve('classification_path'), lids,
resolver.retrieve('classification_path_ranks'))
lineages = [zip(e1, e2, e3) for e1, e2, e3 in lineages]
# make taxdict
taxdict = TaxDict(idents=qnames, ranks=ranks, lineages=lineages)
# get all ranks
allrankids = []
[allrankids.extend(e) for e in lids]
allrankids = [int(e) for e in allrankids] # make sure ints
allrankids = list(set(allrankids))
# init namesdict
namesdict = {}
# loop through taxdict
for key in taxdict.keys():
cident = taxdict[key]['cident'] # Contextual data
if cident:
# if there is context data ....
cname, cident, crank = cident # unpack context name, ID and rank
namesdict[key] = {"txids": [int(cident)], "unique_name": cname,
"rank": crank}
else:
# find unclaimed IDs using allrankids and searching children
rident = taxdict[key]['ident'] # Resolved ID
rank = taxdict[key]['rank'] # Resolved rank
# find ids in the next level
children = etools.findChildren(rident, logger=logger,
next=True)
if children:
unclaimed = [int(e) for e in children]
unclaimed = [e for e in unclaimed if e not in allrankids]
# choose random subset of unclaimed
if len(unclaimed) > 5:
txids = random.sample(unclaimed, 5)
# if there are no unclaimed, just use children
if not unclaimed:
txids = children
if 'txids' not in locals():
# if no unclaimed children, just use rident
txids = [str(rident)]
namesdict[key] = {"txids": txids,
"unique_name": 'Non-unique resolution',
"rank": rank}
# if no parent id given, work one out
if not parentid:
shared_bool = []
for each in lineages[0]:
shared_bool.append(all([each in e for e in lineages]))
parentid = lineages[0][shared_bool.index(False) - 1]
parentid = int(parentid[1]) # second one in tuple
return namesdict, allrankids, parentid
def getOutgroup(namesdict, parentid, logger, outgroupid=None, minrecords=1000):
"""Return namesdict with suitable outgroup"""
# TODO: too complex, consider breaking up
def findParent(parentid):
return etools.eFetch(parentid, logger=logger,
db="taxonomy")[0]['ParentTaxId']
def getTaxIdMetaData(ncbi_id):
etal_bool = False
if len(ncbi_id) > 1:
ncbi_id = ncbi_id[0]
etal_bool = True
record = etools.eFetch(ncbi_id, logger=logger, db="taxonomy")[0]
metadata = [record['Rank'], record['ScientificName']]
if etal_bool:
metadata = [e + ' et al.' for e in metadata]
return metadata[0], metadata[1]
# loop until a suitable outgroup is found. Criteria are:
# 1. ids returned must belong to a sister group of all ids of
# names given
# 2. ids must have nucleotide data (i.e.avoid returning extinct organisms)
# assumptions:
# 1. NCBI taxonomy is not paraphyletic
# make sure parentid is string
if not outgroupid:
parentid = str(parentid)
outgroup_ids = []
while not outgroup_ids:
# if parent id are Cellular Orgs, likely name resolution error
# or names given are too diverse
if parentid == '131567':
raise TaxonomicRankError()
# get parent of parent
grandparentid = findParent(parentid)
# find all children
candidates = etools.findChildren(grandparentid, logger=logger,
next=True)
# filter out children that are in ingroup
candidates = [e for e in candidates if e != parentid]
# search genbank for nuc records
for candidate in candidates:
term = 'txid' + str(candidate) + '[PORGN]'
nuc_record = etools.eSearch(term, logger=logger)
# there must be more than 1000 nuc records
if int(nuc_record['Count']) > minrecords:
outgroup_ids.append(candidate)
# make grandparentid the new parentid
parentid = grandparentid
else:
outgroup_ids = [outgroupid]
# add outgroup_ids to namesdict
rank, unique_name = getTaxIdMetaData(outgroup_ids)
# convert to ints
outgroup_ids = [int(e) for e in outgroup_ids]
namesdict["outgroup"] = {"txids": outgroup_ids, "unique_name": unique_name,
"rank": rank}
return namesdict
