Added documentation

tests/bmlsa/test_aligner.py

@@ -2,7 +2,7 @@ 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 bmlsa.datatypes import QuerySequence
 from collections.abc import Iterable
 
 
@@ -16,7 +16,7 @@ def reference_sequence():
 @pytest.fixture
 def queries():
     return [
-        AlignedSequence(
+        QuerySequence(
             "ORF10",
             "ATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAAT"
             "GAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAG",
@@ -38,8 +38,8 @@ def test_align_many_to_one_returns_correct_data_structure(reference_sequence, qu
         reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
     )
     for original, aligned_seq in results:
-        assert isinstance(original, AlignedSequence)
-        assert isinstance(aligned_seq, AlignedSequence)
+        assert isinstance(original, QuerySequence)
+        assert isinstance(aligned_seq, QuerySequence)
 
 
 def test_align_many_to_one_returns_correct_data(reference_sequence, queries):

tests/bmlsa/test_io.py

@@ -1,21 +1,17 @@
 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 bmlsa.datatypes import QuerySequence
+from bmlsa.io import queries_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"
-    )
+def test_queries_from_csv_has_data():
+    results = queries_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"
-    )
+def test_queries_from_csv_data_valid():
+    results = queries_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)
@@ -23,7 +19,7 @@ def test_read_annotations_from_csv_data_valid():
 
 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")
+    dummy_sequence = QuerySequence("DUMMY", "ATACTGGAAAA", name="test_sequence")
     alignments = [(dummy_sequence, dummy_sequence)]
     save_alignments_to_csv(alignments, output_path)