def test_get_result_paths(self):
"""Tests the function that retrieves the result paths.
aln, sampe, samse, bwasw return only one file.
BWA_index returns 5 files, and the name depends on whether or not the
-p option is on or not
"""
# instantiate objects
index = BWA_index(params = {}, HALT_EXEC=True)
index2 = BWA_index(params = {'-p':'/prefix'}, HALT_EXEC=True)
aln = BWA_aln(params = {'-f':'/sai_out'}, HALT_EXEC=True)
samse = BWA_samse(params = {'-f':'/sam_out'}, HALT_EXEC=True)
sampe = BWA_sampe(params = {'-f':'/sam_out'}, HALT_EXEC=True)
bwasw = BWA_bwasw(params = {'-f':'/sam_out'}, HALT_EXEC=True)
# pass in the data, and make sure the output paths are as expected.
# -p is off here
index_data = {'fasta_in':'/fa_in'}
results = index._get_result_paths(index_data)
self.assertEqual(results['.amb'].Path, '/fa_in.amb')
self.assertEqual(results['.ann'].Path, '/fa_in.ann')
self.assertEqual(results['.bwt'].Path, '/fa_in.bwt')
self.assertEqual(results['.pac'].Path, '/fa_in.pac')
self.assertEqual(results['.sa'].Path, '/fa_in.sa')
# pass in the data, and make sure the output paths are as expected.
# -p is on here
results = index2._get_result_paths(index_data)
self.assertEqual(results['.amb'].Path, '/prefix.amb')
self.assertEqual(results['.ann'].Path, '/prefix.ann')
self.assertEqual(results['.bwt'].Path, '/prefix.bwt')
self.assertEqual(results['.pac'].Path, '/prefix.pac')
self.assertEqual(results['.sa'].Path, '/prefix.sa')
# pass in the data, and make sure the output path is as expected
aln_data = {'prefix':'/fa_in', 'fastq_in':'/fq_in'}
results = aln._get_result_paths(aln_data)
self.assertEqual(results['output'].Path, '/sai_out')
samse_data = {'prefix':'/fa_in', 'sai_in':'/sai_in',
'fastq_in':'/fq_in'}
results = samse._get_result_paths(samse_data)
self.assertEqual(results['output'].Path, '/sam_out')
sampe_data = {'prefix':'/fa_in', 'sai1_in':'/sai1_in',
'sai2_in':'/sai2_in', 'fastq1_in':'/fq1_in',
'fastq2_in':'/fq2_in'}
results = sampe._get_result_paths(sampe_data)
self.assertEqual(results['output'].Path, '/sam_out')
def test_get_result_paths(self):
"""Tests the function that retrieves the result paths.
aln, sampe, samse, bwasw return only one file.
BWA_index returns 5 files, and the name depends on whether or not the
-p option is on or not
"""
# instantiate objects
index = BWA_index(params={}, HALT_EXEC=True)
index2 = BWA_index(params={'-p': '/prefix'}, HALT_EXEC=True)
aln = BWA_aln(params={'-f': '/sai_out'}, HALT_EXEC=True)
samse = BWA_samse(params={'-f': '/sam_out'}, HALT_EXEC=True)
sampe = BWA_sampe(params={'-f': '/sam_out'}, HALT_EXEC=True)
bwasw = BWA_bwasw(params={'-f': '/sam_out'}, HALT_EXEC=True)
# pass in the data, and make sure the output paths are as expected.
# -p is off here
index_data = {'fasta_in': '/fa_in'}
results = index._get_result_paths(index_data)
self.assertEqual(results['.amb'].Path, '/fa_in.amb')
self.assertEqual(results['.ann'].Path, '/fa_in.ann')
self.assertEqual(results['.bwt'].Path, '/fa_in.bwt')
self.assertEqual(results['.pac'].Path, '/fa_in.pac')
self.assertEqual(results['.sa'].Path, '/fa_in.sa')
# pass in the data, and make sure the output paths are as expected.
# -p is on here
results = index2._get_result_paths(index_data)
self.assertEqual(results['.amb'].Path, '/prefix.amb')
self.assertEqual(results['.ann'].Path, '/prefix.ann')
self.assertEqual(results['.bwt'].Path, '/prefix.bwt')
self.assertEqual(results['.pac'].Path, '/prefix.pac')
self.assertEqual(results['.sa'].Path, '/prefix.sa')
# pass in the data, and make sure the output path is as expected
aln_data = {'prefix': '/fa_in', 'fastq_in': '/fq_in'}
results = aln._get_result_paths(aln_data)
self.assertEqual(results['output'].Path, '/sai_out')
samse_data = {
'prefix': '/fa_in',
'sai_in': '/sai_in',
'fastq_in': '/fq_in'
}
results = samse._get_result_paths(samse_data)
self.assertEqual(results['output'].Path, '/sam_out')
sampe_data = {
'prefix': '/fa_in',
'sai1_in': '/sai1_in',
'sai2_in': '/sai2_in',
'fastq1_in': '/fq1_in',
'fastq2_in': '/fq2_in'
}
results = sampe._get_result_paths(sampe_data)
self.assertEqual(results['output'].Path, '/sam_out')
def test_check_arguments(self):
"""Tests the "check_arguments" method of the BWA base class.
Arguments passed to certain parameters of the various subcommands can
take only certain values. The check_arguments function enforces these
constraints. This function ensures that the rules are being enforced
as expected.
"""
# set up test parameters
# should pass
index_params_is = {'-a': 'is'}
# should pass
index_params_bwtsw = {'-a': 'bwtsw'}
# should fail, -a must be one of "is" or "bwtsw"
index_params_invalid = {'-a': 'invalid'}
# should fail, -p must specify a prefix that is an absolute path
index_params_invalid_prefix = {'-p': 'invalid'}
# should pass
index_params_valid_prefix = {'-p': '/prefix'}
# instantiate objects built from the above parameters
index_is = BWA_index(params=index_params_is, HALT_EXEC=True)
index_bwtsw = BWA_index(params=index_params_bwtsw, HALT_EXEC=True)
index_invalid = BWA_index(params=index_params_invalid, HALT_EXEC=True)
index_invalid_prefix = BWA_index(params=index_params_invalid_prefix, \
HALT_EXEC=True)
index_valid_prefix = BWA_index(params=index_params_valid_prefix, \
HALT_EXEC=True)
# Should not be allowed
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
index_invalid.check_arguments)
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
index_invalid_prefix.check_arguments)
# Should execute and not raise any exceptions
index_is.check_arguments()
index_bwtsw.check_arguments()
index_valid_prefix.check_arguments()
# The rest of the _valid_arguments are for checking is_int and is_float
# and they all use the same function from the base-class, so testing
# just one of the subcommands should suffice
# -n must be a float (expressed either as a float or as a string)
# -o must be an int (expressed either as an int or as a string)
# pass, both valid
aln_params_valid = {'-n': 3.0, '-o': 5, '-f':'/sai_out'}
# fail, second invalid
aln_params_invalid1 = {'-n': 3.0, '-o': 'nope', '-f':'/sai_out'}
# fail, first invalid
aln_params_invalid2 = {'-n': '3.5.1', '-o': 4, '-f':'/sai_out'}
# fail, did not specify -f
aln_params_invalid3 = {'-n': 3.0, '-o': 5}
# instantiate objects
aln_valid = BWA_aln(params=aln_params_valid, HALT_EXEC=True)
aln_invalid1 = BWA_aln(params=aln_params_invalid1, HALT_EXEC=True)
aln_invalid2 = BWA_aln(params=aln_params_invalid2, HALT_EXEC=True)
aln_invalid3 = BWA_aln(params=aln_params_invalid3, HALT_EXEC=True)
test_paths = {'prefix': '/fa_in', 'fastq_in': '/fq_in'}
# Should Halt Exec (AssertionError) right before execution
self.assertRaisesRegexp(AssertionError, 'Halted exec', aln_valid,
test_paths)
# also need to make sure the base command is correct
self.assertIn('; bwa aln -f /sai_out -n 3.0 -o 5 /fa_in /fq_in',
aln_valid.BaseCommand)
# Should fail
self.assertRaisesRegexp(ApplicationError,
"Invalid argument", aln_invalid1,
test_paths)
self.assertRaisesRegexp(ApplicationError,
"Invalid argument", aln_invalid2,
test_paths)
self.assertRaisesRegexp(ApplicationError,
"Please specify an output file",
aln_invalid3, test_paths)
def test_check_arguments(self):
"""Tests the "check_arguments" method of the BWA base class.
Arguments passed to certain parameters of the various subcommands can
take only certain values. The check_arguments function enforces these
constraints. This function ensures that the rules are being enforced
as expected.
"""
# set up test parameters
# should pass
index_params_is = {'-a': 'is'}
# should pass
index_params_bwtsw = {'-a': 'bwtsw'}
# should fail, -a must be one of "is" or "bwtsw"
index_params_invalid = {'-a': 'invalid'}
# should fail, -p must specify a prefix that is an absolute path
index_params_invalid_prefix = {'-p': 'invalid'}
# should pass
index_params_valid_prefix = {'-p': '/prefix'}
# instantiate objects built from the above parameters
index_is = BWA_index(params=index_params_is, HALT_EXEC=True)
index_bwtsw = BWA_index(params=index_params_bwtsw, HALT_EXEC=True)
index_invalid = BWA_index(params=index_params_invalid, HALT_EXEC=True)
index_invalid_prefix = BWA_index(params=index_params_invalid_prefix, \
HALT_EXEC=True)
index_valid_prefix = BWA_index(params=index_params_valid_prefix, \
HALT_EXEC=True)
# Should not be allowed
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
index_invalid.check_arguments)
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
index_invalid_prefix.check_arguments)
# Should execute and not raise any exceptions
index_is.check_arguments()
index_bwtsw.check_arguments()
index_valid_prefix.check_arguments()
# The rest of the _valid_arguments are for checking is_int and is_float
# and they all use the same function from the base-class, so testing
# just one of the subcommands should suffice
# -n must be a float (expressed either as a float or as a string)
# -o must be an int (expressed either as an int or as a string)
# pass, both valid
aln_params_valid = {'-n': 3.0, '-o': 5, '-f': '/sai_out'}
# fail, second invalid
aln_params_invalid1 = {'-n': 3.0, '-o': 'nope', '-f': '/sai_out'}
# fail, first invalid
aln_params_invalid2 = {'-n': '3.5.1', '-o': 4, '-f': '/sai_out'}
# fail, did not specify -f
aln_params_invalid3 = {'-n': 3.0, '-o': 5}
# instantiate objects
aln_valid = BWA_aln(params=aln_params_valid, HALT_EXEC=True)
aln_invalid1 = BWA_aln(params=aln_params_invalid1, HALT_EXEC=True)
aln_invalid2 = BWA_aln(params=aln_params_invalid2, HALT_EXEC=True)
aln_invalid3 = BWA_aln(params=aln_params_invalid3, HALT_EXEC=True)
test_paths = {'prefix': '/fa_in', 'fastq_in': '/fq_in'}
# Should Halt Exec (AssertionError) right before execution
self.assertRaisesRegexp(AssertionError, 'Halted exec', aln_valid,
test_paths)
# also need to make sure the base command is correct
self.assertIn('; bwa aln -f /sai_out -n 3.0 -o 5 /fa_in /fq_in',
aln_valid.BaseCommand)
# Should fail
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
aln_invalid1, test_paths)
self.assertRaisesRegexp(ApplicationError, "Invalid argument",
aln_invalid2, test_paths)
self.assertRaisesRegexp(ApplicationError,
"Please specify an output file", aln_invalid3,
test_paths)