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_input_as_dict(self):
"""Tests the input handler (_input_as_dict)
The input handler should throw exceptions if there are not enough
arguments, or if there are unrecognized arguments, or if a file path
appears to be a relative filepath.
"""
# Arguments for BWA_bwasw, which was chosen since it is the only one
# that also has an optional argument (optional arguments are denoted
# by a leading underscore)
missing = {'prefix': '/fa_in', '_query_fasta_2': '/mate'}
extra = {
'prefix': '/fa_in',
'query_fasta': '/query_fasta',
'extra': '/param'
}
rel_fp = {'prefix': 'fa_in', 'query_fasta': '/query_fasta'}
valid = {'prefix': '/fa_in', 'query_fasta': '/query_fasta'}
valid_with_mate = {
'prefix': '/fa_in',
'query_fasta': '/query_fasta',
'_query_fasta_2': '/mate'
}
# instantiate the object
bwasw = BWA_bwasw(params={'-f': '/sam_out'}, HALT_EXEC=True)
# should raise ApplicationError for wrong I/O files; failure
self.assertRaisesRegexp(ApplicationError, "Missing required input",
bwasw, missing)
self.assertRaisesRegexp(ApplicationError, "Invalid input arguments",
bwasw, extra)
self.assertRaisesRegexp(ApplicationError, "Only absolute paths", bwasw,
rel_fp)
# should raise AssertionError (Halt Exec); success
# tests valid arguments with and without the optional
# _query_fasta_2 argument
self.assertRaisesRegexp(AssertionError, 'Halted exec', bwasw, valid)
self.assertRaisesRegexp(AssertionError, 'Halted exec', bwasw,
valid_with_mate)