def get_selection(session, filter_type=None, sample_ids=None):
query = session.query(SelectionPressure).options(
joinedload(SelectionPressure.clone),
joinedload(SelectionPressure.sample),
)
if filter_type == 'overall':
query = query.filter(SelectionPressure.sample_id.is_(None))
elif filter_type == 'samples':
if sample_ids:
query.filter(SelectionPressure.sample_id.in_(sample_ids))
else:
query = query.filter(~SelectionPressure.sample_id.is_(None))
base_fields = SelectionPressure.__table__.c.keys()
base_fields.remove('id')
base_fields.remove('sample_id')
writer = StreamingTSV(['sample', 'subject'] + base_fields)
yield writer.writeheader()
for sel in yield_limit(query, SelectionPressure.id):
row = {f: getattr(sel, f) for f in base_fields}
row['sample'] = sel.sample.name if sel.sample else 'All Samples'
row['subject'] = sel.clone.subject.identifier
yield writer.writerow(row)
def get_sequences(session, sample, fmt, clones_only, min_subject_copies):
meta_keys = set([m.key for m in session.query(SampleMetadata.key)])
seqs = session.query(Sequence).filter(
Sequence.sample_id == sample.id
).join(
SequenceCollapse
).options(
joinedload(Sequence.clone),
joinedload(Sequence.collapse),
joinedload(Sequence.sample),
joinedload(Sequence.subject),
)
if clones_only:
seqs = seqs.filter(~Sequence.clone_id.is_(None))
if min_subject_copies:
seqs = seqs.filter(
SequenceCollapse.copy_number_in_subject >=
min_subject_copies
)
writer = SequenceWriter(fmt, meta_keys)
yield writer.writeheader()
for seq in yield_limit(seqs, Sequence.ai):
yield writer.writeseq(seq)
def get_sequences(session, seqs, format_name):
seqs = seqs.join(SequenceCollapse)
seqs = seqs.options(
joinedload(Sequence.clone),
joinedload(Sequence.collapse),
joinedload(Sequence.sample),
joinedload(Sequence.subject),
)
meta_keys = set([m.key for m in session.query(SampleMetadata.key)])
writer = SequenceWriter(format_name, meta_keys)
yield writer.writeheader()
for seq in yield_limit(seqs, Sequence.ai):
yield writer.writeseq(seq)
def get_clone_summary(session, include_lineages):
fields = [
'clone_id', 'subject', 'v_gene', 'j_gene', 'functional', 'insertions',
'deletions', 'cdr3_nt', 'cdr3_num_nt', 'cdr3_aa', 'uniques',
'instances', 'copies', 'germline', 'parent_id',
'avg_mutations_per_copy'
]
if include_lineages:
fields.append('lineage')
writer = StreamingTSV(fields)
yield writer.writeheader()
for clone in yield_limit(session.query(Clone), Clone.id):
row = {}
for field in writer.fieldnames:
try:
row[field] = getattr(clone, field)
except AttributeError:
pass
row.update({
'clone_id':
clone.id,
'subject':
clone.subject.identifier,
'functional':
'T' if clone.functional else 'F',
'insertions':
clone._insertions,
'deletions':
clone._deletions,
'uniques':
clone.overall_unique_cnt,
'instances':
clone.overall_instance_cnt,
'copies':
clone.overall_total_cnt,
'avg_mutations_per_copy':
round(clone.overall_stats.total_mutations(normalize=True), 2)
})
if include_lineages:
row['lineage'] = clone.tree
yield writer.writerow(row)
def get_clone_overlap(session):
writer = StreamingTSV(
['clone_id', 'sample', 'uniques', 'copies', 'avg_mutations_per_copy'])
stats = session.query(CloneStats).filter(~CloneStats.sample_id.is_(None))
yield writer.writeheader()
for stat in yield_limit(stats, CloneStats.id):
yield writer.writerow({
'clone_id':
stat.clone_id,
'sample':
stat.sample.name,
'uniques':
stat.unique_cnt,
'copies':
stat.total_cnt,
'avg_mutations_per_copy':
round(stat.total_mutations(normalize=True), 2)
})
def get_sequences(session, sample, fmt, clones_only, min_subject_copies):
meta_keys = set([m.key for m in session.query(SampleMetadata.key)])
seqs = session.query(Sequence).filter(
Sequence.sample_id == sample.id).join(SequenceCollapse).options(
joinedload(Sequence.clone),
joinedload(Sequence.collapse),
joinedload(Sequence.sample),
joinedload(Sequence.subject),
)
if clones_only:
seqs = seqs.filter(~Sequence.clone_id.is_(None))
if min_subject_copies:
seqs = seqs.filter(
SequenceCollapse.copy_number_in_subject >= min_subject_copies)
writer = SequenceWriter(fmt, meta_keys)
yield writer.writeheader()
for seq in yield_limit(seqs, Sequence.ai):
yield writer.writeseq(seq)