def test_run_all_fixture_commands(self, test_outdir, commands):
"""This test runs all the commands parameterized in the 'commands'
fixture defined above. (pytest is actually responsible for running the
running this test once for each command / fixture parameter).
Args:
test_outdir (a fixture): This is the output directory into which
all output files are placed.
commands (a parameterized fixture): This boils down to actual
command line arguments given to dupliganger.
"""
# Get the arguments passed
args = docopt(__doc__, help=False, argv=commands.split())
# Fix input file path(s) and outdir path (prepend INFILE_DIR and OUTFILE_DIR)
args = fix_paths(args, INFILE_DIR, OUTFILE_DIR, COMMAND_FILE_PARAMS)
# Get alignment file...
alignment_file = args['<alignment-file>']
# Run dupliganger command!
(parent_db, read_group_db, loc_db) = run(*parse_args(args))
# 13_third_test.sam -> 13_third_test.read_group_db
# 13_third_test.sam -> 13_third_test.read_name_db
# 13_third_test.sam -> 13_third_test.loc_db
for db_name in 'read_group_db loc_db'.split():
# Get string representation of db
db_repr = str(locals()[db_name])
# Get expected out filename
eout = to_eout_db_dump_filename(alignment_file, db_name)
with open(eout, 'r') as e:
assert db_repr == e.read()
def test_run_all_fixture_commands(self, test_outdir, commands):
"""This test runs all the commands parameterized in the 'commands'
fixture defined above. (pytest is actually responsible for running the
running this test once for each command / fixture parameter).
Args:
test_outdir (a fixture): This is the output directory into which
all output files are placed.
commands (a parameterized fixture): This boils down to actual
command line arguments given to dupliganger.
"""
# Get the arguments passed
args = docopt(__doc__, help=False, argv=commands.split())
# Fix input file path(s) and outdir path (prepend INFILE_DIR and OUTFILE_DIR)
args = fix_paths(args, INFILE_DIR, OUTFILE_DIR, COMMAND_FILE_PARAMS)
# Run dupliganger command!
out_files = run(*parse_args(args))
for fout in out_files:
if fout == '/dev/null':
# skip /dev/null's obviously...
continue
# Note that dedup.py uses python's pseudo-random number generator, and
# the RNG differs between py2 and py3, so we pass fix_paths the python
# version to get around this (we have to keep two versions of in/eout
# files, one for py2 and one for py3).
eout = to_eout_filename(fout, sys.version_info[0])
with open(fout, 'r') as f, open(eout, 'r') as e:
assert f.read() == e.read()
def test_run_all_fixture_commands(self, test_outdir, commands):
"""This test runs all the commands parameterized in the 'commands'
fixture defined above. (pytest is actually responsible for running the
running this test once for each command / fixture parameter).
Args:
test_outdir (a fixture): This is the output directory into which
all output files are placed.
commands (a parameterized fixture): This boils down to actual
command line arguments given to dupliganger.
"""
# Get the arguments passed
args = docopt(__doc__, help=False, argv=commands.split())
# Fix input file path(s) and outdir path (prepend INFILE_DIR and OUTFILE_DIR)
args = fix_paths(args, INFILE_DIR, OUTFILE_DIR, COMMAND_FILE_PARAMS)
# Run dupliganger command!
out_files = run(*parse_args(args))
for fout in out_files:
eout = to_eout_filename(fout)
with open(fout, 'r') as f, open(eout, 'r') as e:
assert f.read() == e.read()