def print_sequences(args): db = sqlite3.connect(args.dbname) sql = fetch_reads if args.limit is not None: sql += ' LIMIT {}'.format(args.limit) for defline, blob in db.execute(sql).fetchall(): x = FASTQ(blob) # x._def = "{}".format(rid) x._def = defline x.unpack() print(x)
print('Test Sequence 1:') print(seq1) # Print the attributes: print_info(seq1) # Compress the sequence, print the attributes again: seq1.pack() print_info(seq1) # We should be able to restore the original attributes: seq1.unpack() print_info(seq1) # Create another FASTQ object, this time from a byte array (e.g. a blob # written into a database). The sequence will have an empty defline, so # we need to add one: seq2 = FASTQ(b'\xc8P\x1e\x1e\xb4\xc8\xb9UU#') seq2._def = 'restored sequence' seq2.unpack() print('\nTest Sequence 2:') print(seq2) print() # This test shows how to read sequences from a file using the FASTQReader class.