def test_merge_1_insertion_2_subsets_0():
test_root = "./test/merge_test/merge_1_insertion_2_subsets_0/"
test_suffix = "merge_1_insertion_2_subsets_0/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
merged_alignment = main.merge_hmms_helper(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "bitscore+size", "DNA", "FASTA", False)
assert merged_alignment == {
"fragment": "AAAAtAAAA",
"s1": "AAAA-AAAA",
"s2": "AAAA-AAAA",
"s3": "AAAA-AAAA",
"s4": "AAAA-AAAA",
"s5": "AAAA-AAAA",
"s6": "AAAA-AAAA",
"s7": "AAAA-AAAA",
"s8": "AAAA-AAAA",
"backbone_indices": [1, 2, 3, 4, "I", 5, 6, 7, 8],
}
def test_merge_2_subsets_0():
test_root = "./test/merge_test/merge_2_subsets_0/"
test_suffix = "merge_2_subsets_0/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
merged_alignment = main.merge_hmms_helper(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "bitscore+size", "DNA", "FASTA", False)
assert merged_alignment == {
"fragment": "AAAAAAAA----------------------",
"s1": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s2": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s3": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s4": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s5": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s6": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s7": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"s8": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"backbone_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30],
}