def query_by_sqlite(self, queries, db):
max_set_size = 999 # Cannot query sqlite with > 999 '?' entries, so
# query in batches.
sequence_to_query_id = {}
queries_list = list(queries)
seqs = set()
for i, query in enumerate(queries_list):
seqs.add(query.sequence)
try:
sequence_to_query_id[query.sequence].append(i)
except KeyError:
sequence_to_query_id[query.sequence] = [i]
results = []
for chunk in SequenceDatabase.grouper(seqs, max_set_size):
for entry in db.table('otus').where_in(
'sequence',
[seq for seq in chunk if seq is not None]).get():
for qid in sequence_to_query_id[entry.sequence]:
otu = OtuTableEntry()
otu.marker = entry.marker
otu.sample_name = entry.sample_name
otu.sequence = entry.sequence
otu.count = entry.num_hits
otu.coverage = entry.coverage
otu.taxonomy = entry.taxonomy
results.append(QueryResult(queries_list[qid], otu, 0))
return results
def query(self, **kwargs):
db = SequenceDatabase.acquire(kwargs.pop('db'))
query_sequence = kwargs.pop('query_sequence')
max_divergence = kwargs.pop('max_divergence')
output_style = kwargs.pop('output_style')
query_otu_table = kwargs.pop('query_otu_table')
query_fasta = kwargs.pop('query_fasta')
num_threads = kwargs.pop('num_threads')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if (query_otu_table and query_sequence) or \
(query_otu_table and query_fasta) or \
(query_sequence and query_fasta):
raise Exception(
"Only one of --query_fasta, --query_otu_table and --query_sequence is allowable"
)
queries = self.prepare_query_sequences(query_sequence, query_otu_table,
query_fasta)
logging.info("Read in %i queries" % len(queries))
query_results = self.query_with_queries(queries, db, max_divergence)
logging.info("Printing %i hits" % len(query_results))
if output_style == 'sparse':
SparseResultFormatter().write(query_results, sys.stdout)
elif output_style == None:
return query_results
else:
raise Exception("Programming error")
def query_by_sqlite(self, queries, db):
max_set_size = 999 # Cannot query sqlite with > 999 '?' entries, so
# query in batches.
sequence_to_query_id = {}
queries_list = list(queries)
seqs = set()
for i, query in enumerate(queries_list):
seqs.add(query.sequence)
try:
sequence_to_query_id[query.sequence].append(i)
except KeyError:
sequence_to_query_id[query.sequence] = [i]
results = []
for chunk in SequenceDatabase.grouper(seqs, max_set_size):
for entry in db.table('otus').where_in(
'sequence', [seq for seq in chunk if seq is not None]).get():
for qid in sequence_to_query_id[entry.sequence]:
otu = OtuTableEntry()
otu.marker = entry.marker
otu.sample_name = entry.sample_name
otu.sequence = entry.sequence
otu.count = entry.num_hits
otu.coverage = entry.coverage
otu.taxonomy = entry.taxonomy
results.append(QueryResult(queries_list[qid], otu, 0))
return results
def query(self, **kwargs):
db = SequenceDatabase.acquire(kwargs.pop('db'))
query_sequence = kwargs.pop('query_sequence')
max_divergence = kwargs.pop('max_divergence')
output_style = kwargs.pop('output_style')
query_otu_table = kwargs.pop('query_otu_table')
query_fasta = kwargs.pop('query_fasta')
num_threads = kwargs.pop('num_threads')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if (query_otu_table and query_sequence) or \
(query_otu_table and query_fasta) or \
(query_sequence and query_fasta):
raise Exception("Only one of --query_fasta, --query_otu_table and --query_sequence is allowable")
queries = self.prepare_query_sequences(
query_sequence, query_otu_table, query_fasta)
logging.info("Read in %i queries" % len(queries))
query_results = self.query_with_queries(queries, db, max_divergence)
logging.info("Printing %i hits" % len(query_results))
if output_style == 'sparse':
SparseResultFormatter().write(query_results, sys.stdout)
elif output_style == None:
return query_results
else:
raise Exception("Programming error")
def print_samples(self, **kwargs):
db = SequenceDatabase.acquire(kwargs.pop('db'))
sample_names = kwargs.pop('sample_names')
taxonomy = kwargs.pop('taxonomy')
output_io = kwargs.pop('output_io')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
dbm = self._connect_to_sqlite(db)
max_set_size = 999 # Cannot query sqlite with > 999 '?' entries, so
# query in batches.
if sample_names:
query_chunks = set(sample_names)
else:
query_chunks = [taxonomy]
otus = OtuTable()
total_printed = 0
for chunk in SequenceDatabase.grouper(query_chunks, max_set_size):
if sample_names:
it = dbm.table('otus').where_in(
'sample_name',
[sample for sample in chunk if sample is not None]).get()
elif taxonomy:
it = dbm.table('otus').where('taxonomy', 'like',
"%%%s%%" % taxonomy).get()
else:
raise Exception("Programming error")
for entry in it:
otu = OtuTableEntry()
otu.marker = entry.marker
otu.sample_name = entry.sample_name
otu.sequence = entry.sequence
otu.count = entry.num_hits
otu.coverage = entry.coverage
otu.taxonomy = entry.taxonomy
otus.add([otu])
total_printed += 1
otus.write_to(output_io)
logging.info("Printed %i OTU table entries" % total_printed)
def print_samples(self, **kwargs):
db = SequenceDatabase.acquire(kwargs.pop('db'))
sample_names = kwargs.pop('sample_names')
taxonomy = kwargs.pop('taxonomy')
output_io = kwargs.pop('output_io')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
dbm = self._connect_to_sqlite(db)
max_set_size = 999 # Cannot query sqlite with > 999 '?' entries, so
# query in batches.
if sample_names:
query_chunks = set(sample_names)
else:
query_chunks = [taxonomy]
otus = OtuTable()
total_printed = 0
for chunk in SequenceDatabase.grouper(query_chunks, max_set_size):
if sample_names:
it = dbm.table('otus').where_in(
'sample_name', [sample for sample in chunk if sample is not None]).get()
elif taxonomy:
it = dbm.table('otus').where(
'taxonomy', 'like', "%%%s%%" % taxonomy).get()
else:
raise Exception("Programming error")
for entry in it:
otu = OtuTableEntry()
otu.marker = entry.marker
otu.sample_name = entry.sample_name
otu.sequence = entry.sequence
otu.count = entry.num_hits
otu.coverage = entry.coverage
otu.taxonomy = entry.taxonomy
otus.add([otu])
total_printed += 1
otus.write_to(output_io)
logging.info("Printed %i OTU table entries" % total_printed)