Many changes, see details:

Now allow for changing whether alignment is local or global and various scoring parameters

Refactored directory structure

Removed redundant aligned dict pattern for simple iterable

Added unit tests

tests/bmlsa/test_aligner.py

@@ -0,0 +1,51 @@
+import pytest
+from Bio import SeqIO
+from bmlsa.aligner import align_many_to_one_ssw
+from bmlsa.cli import DEFAULT_ALIGNMENT_PARAMETERS
+from bmlsa.datatypes import AlignedSequence
+from collections.abc import Iterable
+
+
+@pytest.fixture
+def reference_sequence():
+    return str(
+        list(SeqIO.parse("tests/resources/NC_045512_coding.fasta", "fasta"))[0].seq
+    )
+
+
+@pytest.fixture
+def queries():
+    return [
+        AlignedSequence(
+            "ORF10",
+            "ATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAAT"
+            "GAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAG",
+            start=29558,
+            end=29674,
+        )
+    ]
+
+
+def test_align_many_to_one_returns_data(reference_sequence, queries):
+    results = align_many_to_one_ssw(
+        reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
+    )
+    assert isinstance(results, Iterable)
+
+
+def test_align_many_to_one_returns_correct_data_structure(reference_sequence, queries):
+    results = align_many_to_one_ssw(
+        reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
+    )
+    for original, aligned_seq in results:
+        assert isinstance(original, AlignedSequence)
+        assert isinstance(aligned_seq, AlignedSequence)
+
+
+def test_align_many_to_one_returns_correct_data(reference_sequence, queries):
+    results = align_many_to_one_ssw(
+        reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
+    )
+    for original, aligned_seq in results:
+        assert original.start == aligned_seq.start
+        assert original.end == aligned_seq.end

tests/bmlsa/test_io.py

@@ -0,0 +1,35 @@
+from csv import reader
+from os import path
+from bmlsa.datatypes import AlignedSequence
+from bmlsa.io import read_annotations_from_csv, save_alignments_to_csv
+from collections.abc import Iterable
+
+
+def test_read_annotations_from_csv_has_data():
+    results = read_annotations_from_csv(
+        "tests/resources/SARS_CoV-2_genes.csv", "id", "sequence"
+    )
+    assert isinstance(results, Iterable)
+
+
+def test_read_annotations_from_csv_data_valid():
+    results = read_annotations_from_csv(
+        "tests/resources/SARS_CoV-2_genes.csv", "id", "sequence"
+    )
+    for aligned_seq in results:
+        assert isinstance(aligned_seq.id, str)
+        assert isinstance(aligned_seq.sequence, str)
+
+
+def test_save_alignments_to_csv_produces_correct_headers_in_csv(tmpdir):
+    output_path = path.join(tmpdir, "alignment_results.csv")
+    dummy_sequence = AlignedSequence("DUMMY", "ATACTGGAAAA", name="test_sequence")
+    alignments = [(dummy_sequence, dummy_sequence)]
+    save_alignments_to_csv(alignments, output_path)
+
+    with open(output_path, "r") as csv_fd:
+        results = list(reader(csv_fd))
+        vars_to_check = list(vars(dummy_sequence).keys())
+        for var_to_check in vars_to_check:
+            assert "original" + var_to_check in results[0]
+            assert "aligned" + var_to_check in results[0]