def test_creates_fresh_reads_file(self, path_reads_file, require_aligned,
remove_reads_file):
""" Reads file pysam object is created by register_files(). """
# Note that remove_reads_file is here to clear the module-scoped map.
# Explicitly set by_chromosome=False to prevent it from
# controlling the requirement regarding aligned reads.
processor = IdentityProcessor(path_reads_file=path_reads_file,
action="test",
allow_unaligned=not require_aligned,
by_chromosome=False)
# The pysam readsfile shouldn't exist before register_files().
with pytest.raises(CommandOrderException):
processor.readsfile
# Now do the registration, creating the pysam readsfile instance.
processor.register_files()
readsfile = processor.readsfile
# Check out the new readsfile.
assert isinstance(readsfile, AlignmentFile)
num_reads = sum(1 for _ in readsfile)
assert NUM_READS_BY_FILE[path_reads_file] == num_reads
def test_adds_pysam_kwargs(self, require_aligned, pysam_kwargs,
remove_reads_file):
""" Unaligned input BAM needs check_sq=False to be created. """
# Note that remove_reads_file is here to clear the module-scoped map.
# Explicitly set by_chromosome=False to prevent it from
# controlling the requirement regarding aligned reads.
processor = IdentityProcessor(path_reads_file=PATH_UNALIGNED_FILE,
action="test",
allow_unaligned=not require_aligned,
by_chromosome=False)
if require_aligned:
exp_error = MissingHeaderException if pysam_kwargs else ValueError
with pytest.raises(exp_error):
processor.register_files(**pysam_kwargs)
else:
# No exception --> pass (file registration is just for effect.)
processor.register_files(**pysam_kwargs)