def write_record(self, individual, data_samples,
data_collection_samples=None):
allele_patterns = {0: 'AA', 1: 'BB', 2:'AB', 3: 'NN'}
if data_collection_samples:
dsamples = [d for d in data_samples if d in data_collection_samples]
else:
dsamples = data_samples
if len(dsamples) > 0:
if self.igd:
dsamples = dsamples[:1]
for ds in dsamples:
start = time.time()
probs, _ = ds.resolve_to_data()
end = time.time() - start
self.counter['total_fetch_time'] += end
if end < self.counter['faster_fetch'] or 'faster_fetch' not in self.counter:
self.counter['faster_fetch'] = end
if end > self.counter['slower_fetch']:
self.counter['slower_fetch'] = end
self.logger.debug('Retrieved data for %s in %f seconds' %
(ds.label, end))
if probs is not None:
self.counter['fetched_samples'] += 1
self.out_ds_csvw.writerow([ds.id])
disc_probs = [allele_patterns[x]
for x in project_to_discrete_genotype(probs)]
if self.tro:
self.out_gt_csvw.writerow(disc_probs)
else:
self.out_data.append(disc_probs)
def dump_genotype(fo, data_sample):
if data_sample is None:
probs = self.null_probs
else:
probs, _ = data_sample.resolve_to_data()
if self.selected_markers:
probs = probs[:, self.selected_markers]
fo.write('\t'.join([allele_patterns[x]
for x in project_to_discrete_genotype(probs)]))
fo.write('\n')
def write_record(self,
individual,
data_samples,
data_collection_samples=None):
allele_patterns = {0: 'AA', 1: 'BB', 2: 'AB', 3: 'NN'}
if data_collection_samples:
dsamples = [
d for d in data_samples if d in data_collection_samples
]
else:
dsamples = data_samples
if len(dsamples) > 0:
if self.igd:
dsamples = dsamples[:1]
for ds in dsamples:
start = time.time()
probs, _ = ds.resolve_to_data()
end = time.time() - start
self.counter['total_fetch_time'] += end
if end < self.counter[
'faster_fetch'] or 'faster_fetch' not in self.counter:
self.counter['faster_fetch'] = end
if end > self.counter['slower_fetch']:
self.counter['slower_fetch'] = end
self.logger.debug('Retrieved data for %s in %f seconds' %
(ds.label, end))
if probs is not None:
self.counter['fetched_samples'] += 1
self.out_ds_csvw.writerow([ds.id])
disc_probs = [
allele_patterns[x]
for x in project_to_discrete_genotype(probs)
]
if self.tro:
self.out_gt_csvw.writerow(disc_probs)
else:
self.out_data.append(disc_probs)
