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test.py
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import main
import os
import shutil
TEMP_OUTPUT_PREFIX = "./tmp/"
def setup_mapping_inputs(test_root, num_subsets):
input_fasta_filenames = {}
for i in range(num_subsets):
input_fasta_filenames[i] = test_root + "input_" + str(i) + ".fasta"
backbone_alignment = test_root + "backbone.fasta"
return input_fasta_filenames,backbone_alignment
def setup_merge_inputs(test_root, test_suffix):
backbone_alignment = test_root + "backbone.fasta"
fragment_sequences_file = test_root + "fragment.fasta"
if os.path.exists(TEMP_OUTPUT_PREFIX + test_suffix):
shutil.rmtree(TEMP_OUTPUT_PREFIX + test_suffix)
os.mkdir(TEMP_OUTPUT_PREFIX + test_suffix)
return test_root,backbone_alignment,fragment_sequences_file,test_root
def test_merge_1_insertion_1_fragment_5_subsets_0():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_0/"
test_suffix = "merge_1_insertion_1_fragment_5_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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "tAAAAA",
"s1": "-AAAAA",
"s2": "-AAAAA",
"s3": "-AAAAA",
"s4": "-AAAAA",
"s5": "-AAAAA",
"s6": "-AAAAA",
"s7": "-AAAAA",
"s8": "-AAAAA",
"s9": "-AAAAA",
"s10": "-AAAAA",
"backbone_indices": ["I", 1, 2, 3, 4, 5],
}
def test_merge_1_insertion_1_fragment_5_subsets_1():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_1/"
test_suffix = "merge_1_insertion_1_fragment_5_subsets_1/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AtAAAA",
"s1": "A-AAAA",
"s2": "A-AAAA",
"s3": "A-AAAA",
"s4": "A-AAAA",
"s5": "A-AAAA",
"s6": "A-AAAA",
"s7": "A-AAAA",
"s8": "A-AAAA",
"s9": "A-AAAA",
"s10": "A-AAAA",
"backbone_indices": [1, "I", 2, 3, 4, 5],
}
def test_merge_1_insertion_1_fragment_5_subsets_2():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_2/"
test_suffix = "merge_1_insertion_1_fragment_5_subsets_2/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAtAAA",
"s1": "AA-AAA",
"s2": "AA-AAA",
"s3": "AA-AAA",
"s4": "AA-AAA",
"s5": "AA-AAA",
"s6": "AA-AAA",
"s7": "AA-AAA",
"s8": "AA-AAA",
"s9": "AA-AAA",
"s10": "AA-AAA",
"backbone_indices": [1, 2, "I", 3, 4, 5],
}
def test_merge_1_insertion_1_fragment_5_subsets_3():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_3/"
test_suffix = "merge_1_insertion_1_fragment_5_subsets_3/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAAtAA",
"s1": "AAA-AA",
"s2": "AAA-AA",
"s3": "AAA-AA",
"s4": "AAA-AA",
"s5": "AAA-AA",
"s6": "AAA-AA",
"s7": "AAA-AA",
"s8": "AAA-AA",
"s9": "AAA-AA",
"s10": "AAA-AA",
"backbone_indices": [1, 2, 3, "I", 4, 5],
}
def test_merge_1_insertion_1_fragment_5_subsets_4():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_4/"
test_suffix = "merge_1_insertion_1_fragment_5_subsets_4/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAAAtA",
"s1": "AAAA-A",
"s2": "AAAA-A",
"s3": "AAAA-A",
"s4": "AAAA-A",
"s5": "AAAA-A",
"s6": "AAAA-A",
"s7": "AAAA-A",
"s8": "AAAA-A",
"s9": "AAAA-A",
"s10": "AAAA-A",
"backbone_indices": [1, 2, 3, 4, "I", 5],
}
def test_merge_1_insertion_1_fragment_5_subsets_5():
test_root = "./test/merge_test/merge_1_insertion_1_fragment_5_subsets_5/"
test_suffix = "merge_1_insertion_1_fragment_5_subsets_5/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAAAAt",
"s1": "AAAAA-",
"s2": "AAAAA-",
"s3": "AAAAA-",
"s4": "AAAAA-",
"s5": "AAAAA-",
"s6": "AAAAA-",
"s7": "AAAAA-",
"s8": "AAAAA-",
"s9": "AAAAA-",
"s10": "AAAAA-",
"backbone_indices": [1, 2, 3, 4, 5, "I"],
}
def test_merge_7_insertion_1_fragment_5_subsets_0():
test_root = "./test/merge_test/merge_7_insertion_1_fragment_5_subsets_0/"
test_suffix = "merge_7_insertion_1_fragment_5_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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "tttttttAAAAA",
"s1": "-------AAAAA",
"s2": "-------AAAAA",
"s3": "-------AAAAA",
"s4": "-------AAAAA",
"s5": "-------AAAAA",
"s6": "-------AAAAA",
"s7": "-------AAAAA",
"s8": "-------AAAAA",
"s9": "-------AAAAA",
"s10": "-------AAAAA",
"backbone_indices": ["I", "I", "I", "I", "I", "I", "I", 1, 2, 3, 4, 5],
}
def test_merge_5_insertion_1_fragment_5_subsets_0():
test_root = "./test/merge_test/merge_5_insertion_1_fragment_5_subsets_0/"
test_suffix = "merge_5_insertion_1_fragment_5_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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAtttttAAA",
"s1": "AA-----AAA",
"s2": "AA-----AAA",
"s3": "AA-----AAA",
"s4": "AA-----AAA",
"s5": "AA-----AAA",
"s6": "AA-----AAA",
"s7": "AA-----AAA",
"s8": "AA-----AAA",
"s9": "AA-----AAA",
"s10": "AA-----AAA",
"backbone_indices": [1, 2, "I", "I", "I", "I", "I", 3, 4, 5],
}
def test_merge_1_insertion_2_fragments_2_subsets_0():
test_root = "./test/merge_test/merge_1_insertion_2_fragments_2_subsets_0/"
test_suffix = "merge_1_insertion_2_fragments_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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment-0": "A-AAAtAAAA",
"fragment-1": "AtAAA-AAAA",
"s1": "A-AAA-AAAA",
"s2": "A-AAA-AAAA",
"s3": "A-AAA-AAAA",
"s4": "A-AAA-AAAA",
"s5": "A-AAA-AAAA",
"s6": "A-AAA-AAAA",
"s7": "A-AAA-AAAA",
"s8": "A-AAA-AAAA",
"backbone_indices": [1, "I", 2, 3, 4, "I", 5, 6, 7, 8],
}
def test_merge_1_insertion_2_fragments_2_subsets_1():
test_root = "./test/merge_test/merge_1_insertion_2_fragments_2_subsets_1/"
test_suffix = "merge_1_insertion_2_fragments_2_subsets_1/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment-0": "A-AAAtAAAAGGGGGGGGGGGGGGGGGGGG",
"fragment-1": "TaTTT-TTTTGGGGGGGGGGGGGGGGGGGG",
"s1": "A-AAA-AAAAGGGGGGGGGGGGGGGGGGGG",
"s2": "A-AAA-AAAAGGGGGGGGGGGGGGGGGGGG",
"s3": "A-AAA-AAAAGGGGGGGGGGGGGGGGGGGG",
"s4": "A-AAA-AAAAGGGGGGGGGGGGGGGGGGGG",
"s5": "T-TTT-TTTTGGGGGGGGGGGGGGGGGGGG",
"s6": "T-TTT-TTTTGGGGGGGGGGGGGGGGGGGG",
"s7": "T-TTT-TTTTGGGGGGGGGGGGGGGGGGGG",
"s8": "T-TTT-TTTTGGGGGGGGGGGGGGGGGGGG",
"backbone_indices": [1, "I", 2, 3, 4, "I", 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28],
}
def test_merge_1_insertion_2_fragments_2_subsets_2():
test_root = "./test/merge_test/merge_1_insertion_2_fragments_2_subsets_2/"
test_suffix = "merge_1_insertion_2_fragments_2_subsets_2/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment-0": "AAAAt----AAAAGGGGGGGGGGGGGGGGGGGG",
"fragment-1": "TTTT-atttTTTTGGGGGGGGGGGGGGGGG---",
"s1": "AAAA-----AAAAGGGGGGGGGGGGGGGGGGGG",
"s2": "AAAA-----AAAAGGGGGGGGGGGGGGGGGGGG",
"s3": "AAAA-----AAAAGGGGGGGGGGGGGGGGGGGG",
"s4": "AAAA-----AAAAGGGGGGGGGGGGGGGGGGGG",
"s5": "TTTT-----TTTTGGGGGGGGGGGGGGGGGGGG",
"s6": "TTTT-----TTTTGGGGGGGGGGGGGGGGGGGG",
"s7": "TTTT-----TTTTGGGGGGGGGGGGGGGGGGGG",
"s8": "TTTT-----TTTTGGGGGGGGGGGGGGGGGGGG",
"backbone_indices": [1, 2, 3, 4, "I", "I", "I", "I", "I", 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28],
}
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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
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
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
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],
}
def test_merge_2_subsets_2_match_regions():
test_root = "./test/merge_test/merge_2_subsets_2_match_regions/"
test_suffix = "merge_2_subsets_2_match_regions/"
input_dir,backbone_alignment,fragment_sequences_file,test_root = setup_merge_inputs(test_root, test_suffix)
output_prefix = TEMP_OUTPUT_PREFIX + test_suffix
hmmerge = main.HMMerge(input_dir, backbone_alignment, fragment_sequences_file, output_prefix, "custom", 1, 1.0, "DNA", "FASTA", False)
merged_alignment = hmmerge.merge_hmms_helper()
assert merged_alignment == {
"fragment": "AAAATTTTGGGGG",
"s1": "----TTTTGGGGG",
"s2": "----TTTTGGGGG",
"s3": "----TTTTGGGGG",
"s4": "AAAA----GGGGG",
"s5": "AAAA----GGGGG",
"s6": "AAAA----GGGGG",
"backbone_indices": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13],
}