def _check_results_prep_2(self):
self._check_no_error_results()
command_stdout_file_name = self._get_stdout_file_name()
with open(command_stdout_file_name, 'rt') as out_f_h:
out_lines = out_f_h.readlines()
tests.util.assert_no_line_has(self, out_lines,
'Processing count files')
test_gene_id = tests.util.gene_id_str(1)
quoted_test_gene_id = tests.util.double_quote(test_gene_id)
dot_rmats_paths = self._get_dot_rmats_paths(self._prep_2_tmp_dir)
self.assertEqual(len(dot_rmats_paths), 2)
for dot_rmats_i in range(2):
dot_rmats_contents, error = output_parser.parse_dot_rmats(
dot_rmats_paths[dot_rmats_i])
self.assertFalse(error)
self.assertEqual(dot_rmats_contents['bams'],
[self._sample_2_bams[dot_rmats_i].path])
self.assertEqual(dot_rmats_contents['read_length'],
self._read_length)
novel_juncs = dot_rmats_contents['novel_juncs']
self.assertEqual(novel_juncs, [{quoted_test_gene_id: [[0, 0, 2]]}])
exons = dot_rmats_contents['exons']
if dot_rmats_i == 0:
self.assertEqual(exons, [{
quoted_test_gene_id: [{
'start_box': [401, 499],
'end_box': [401, 499],
'counts': [1, 0]
}]
}])
else:
self.assertEqual(exons, [{
quoted_test_gene_id: [{
'start_box': [1, 99],
'end_box': [1, 99],
'counts': [1, 0]
}]
}])
multis = dot_rmats_contents['multis']
if dot_rmats_i == 0:
self.assertEqual(multis, [{
quoted_test_gene_id: [{
'junction_pairs': [[1, 1], [100, 400], [499, 499]],
'count':
1
}]
}])
else:
self.assertEqual(multis, [{
quoted_test_gene_id: [{
'junction_pairs': [[1, 1], [100, 400], [499, 499]],
'count':
1
}]
}])
self._cp_with_prefix('prep_2_', self._prep_2_tmp_dir,
self._post_tmp_dir)
def _check_results_prep_1(self):
self._check_no_error_results()
command_stdout_file_name = self._get_stdout_file_name()
with open(command_stdout_file_name, 'rt') as out_f_h:
out_lines = out_f_h.readlines()
tests.util.assert_no_line_has(self, out_lines,
'Processing count files')
dot_rmats_paths = self._get_dot_rmats_paths(self._prep_1_tmp_dir)
self.assertEqual(len(dot_rmats_paths), 1)
dot_rmats_contents, error = output_parser.parse_dot_rmats(
dot_rmats_paths[0])
self.assertFalse(error)
self.assertEqual(dot_rmats_contents['bams'],
[bam.path for bam in self._sample_1_bams])
self.assertEqual(dot_rmats_contents['read_length'], self._read_length)
test_gene_id = tests.util.gene_id_str(1)
quoted_test_gene_id = tests.util.double_quote(test_gene_id)
novel_juncs = dot_rmats_contents['novel_juncs']
self.assertEqual(len(novel_juncs), 2)
self.assertEqual(novel_juncs[0], {})
self.assertEqual(novel_juncs[1], {})
exons = dot_rmats_contents['exons']
self.assertEqual(len(exons), 2)
self.assertEqual(
exons[0], {
quoted_test_gene_id: [{
'start_box': [401, 499],
'end_box': [401, 499],
'counts': [1, 0]
}]
})
self.assertEqual(
exons[1], {
quoted_test_gene_id: [{
'start_box': [1, 99],
'end_box': [1, 99],
'counts': [1, 0]
}]
})
multis = dot_rmats_contents['multis']
self.assertEqual(len(multis), 2)
self.assertEqual(
multis[0], {
quoted_test_gene_id: [{
'junction_pairs': [[1, 1], [100, 200], [299, 299]],
'count':
1
}]
})
self.assertEqual(
multis[1], {
quoted_test_gene_id: [{
'junction_pairs': [[201, 201], [300, 400], [499, 499]],
'count':
1
}]
})
self._cp_with_prefix('prep_1_', self._prep_1_tmp_dir,
self._post_tmp_dir)