def get_shared_amino_acids_counts(self, **kwargs):
'''
Given a comparison, returns the amino acids shared by all clonofilters within a comparison
By default returns the first 10 results, but can return different page
or number of results by modifying kwargs
Returns a nested dict in the format:
{aa1_id: {'sequence': aa.sequence, 'clonofiters':{ cf_id1: float,
cf_id2: float,}}
'''
from clonotypes.models import AminoAcid
from collections import defaultdict
from django.db.models import Q
# Get a list of clonofilters
clonofilters = self.clonofilters_all()
# Get a list of sample ids
samples = self.get_samples()
# Get a dict of sample id to clonofilter ids
sampleid2cfid = defaultdict(lambda: [])
for cf in clonofilters:
sampleid2cfid[cf.sample.id].append(cf.id)
# prefect clonofilters and index by their id
cfid2cf = dict((cf.id, cf) for cf in clonofilters)
# Set up the paginator
try:
paginator = Paginator(self.get_shared_amino_acids(), kwargs['per_page'])
except:
paginator = Paginator(self.get_shared_amino_acids(), 10)
# Get the page number
try:
shared_amino_acids = paginator.page(kwargs['page'])
except EmptyPage:
shared_amino_acids = paginator.page(paginator.num_pages)
except:
shared_amino_acids = paginator.page(1)
# Get all nucleotide_sequences belonging to samples and then only report those
# that have at least len(samples) shared clonotypes
returnable = {}
#for amino_acid in shared_amino_acids:
for amino_acid in shared_amino_acids:
amino_acid_dict = {}
clonofilter_dict = defaultdict(lambda: 0)
for recombination in amino_acid.recombination_set.all():
for clonotype in recombination.clonotype_set.all():
if clonotype.sample in samples:
for cfid in sampleid2cfid[clonotype.sample.id]:
clonofilter_dict[cfid] += 1.0*clonotype.count/cfid2cf[cfid].size()
amino_acid_dict['clonofilters'] = undefaulted(clonofilter_dict)
amino_acid_dict['sequence'] = amino_acid.sequence
returnable[amino_acid.id] = amino_acid_dict
return returnable, paginator.num_pages, paginator.count
def hits_by_article(self):
'''
Returns a dict of BlatHit objects where an article is the key
'''
from collections import defaultdict
from utils.utils import undefaulted
hit_dict = defaultdict(list)
hits = self.hits();
for hit in hits:
hit_dict[hit.article].append(hit);
return undefaulted(hit_dict)
def get_shared_recombinations_counts(self):
'''
Given a comparison, returns the recombinations shared by all samples
Returns a nested dict in the format:
{'recombination.id': {'clonofilter': <sum_of_norm_counts>, 'clonofilter2': <sum of norm counts>}}
'''
from clonotypes.models import Recombination
from collections import defaultdict
# Get all nucleotide_sequences belonging to samples and then only report those
# that have at least len(samples) shared clonotypes
returnable = defaultdict(lambda: defaultdict(lambda: .0))
# Get a list of clonofilters
clonofilters = self.clonofilters_all()
# Get a list of sample ids
samples = self.get_samples()
if len(samples) > 1:
# Now get all clonotypes with these shared sequences
shared_recombinations = reduce(lambda q, s: q.filter(
clonotype__sample=s), samples, self.get_recombinations())
shared_recombination = shared_recombinations.distinct()
# Format the shared clonotypes as a dict of lists:
# {'sequence': [<clonotype 1>, <clonotype2>]}
for recombination in shared_recombinations:
# Get the set of clonotypes for each recombination
for clonotype in recombination.clonotype_set.all():
if clonotype.sample in samples:
returnable[recombination.nucleotide][
clonotype.sample] += clonotype.count
# Get the set of samples for each clonotype
# Add # of reads per thing
# returnable[recombination.nucleotide].append(clonotype)
return undefaulted(returnable)
def get_shared_amino_acids_clonotypes(self):
'''
Given a comparison, returns the amino acids shared by all clonofilters within a comparison
Returns a nested dict in the format:
{'amino_acid': {'clonofilter': <sum_of_norm_counts>, 'clonofilter2': <sum of norm counts>}}
'''
from clonotypes.models import AminoAcid
from collections import defaultdict
from django.db.models import Q
# Get a list of sample ids
samples = self.get_samples()
# Get all nucleotide_sequences belonging to samples and then only report those
# that have at least len(samples) shared clonotypes
returnable = defaultdict(lambda: defaultdict(lambda: .0))
shared_amino_acid = self.get_shared_amino_acids()
if shared_amino_acid:
for amino_acid in shared_amino_acid:
for recombination in amino_acid.recombination_set.all():
for clonotype in recombination.clonotype_set.all():
if clonotype.sample in samples:
returnable[
amino_acid][clonotype.sample] = clonotype
return undefaulted(returnable)
