except NameError: # Python 2 does not have this, FileNotFoundError = IOError from Bio.SeqRecord import SeqRecord from Bio import SeqIO from Bio.SeqIO._index import _FormatToRandomAccess from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna from seq_tests_common import compare_record from Bio import BiopythonParserWarning from Bio import MissingPythonDependencyError try: from test_bgzf import _have_bug17666 do_bgzf = _have_bug17666() except MissingPythonDependencyError: do_bgzf = False CUR_DIR = os.getcwd() def add_prefix(key): """Dummy key_function for testing index code.""" return "id_" + key def gzip_open(filename, format): # At time of writing, under Python 3.2.2 seems gzip.open(filename, mode) # insists on giving byte strings (i.e. binary mode) # See http://bugs.python.org/issue13989