add test_sequence

tests/test_sequence.py

@@ -0,0 +1,27 @@
+from Bio import SeqIO
+from pathlib import Path
+import os
+import pytest
+
+from arctic3d.modules.sequence import cycle_alignment
+
+from . import golden_data
+
+
+@pytest.fixture
+def inp_fasta():
+    return Path(golden_data, "1rypB_r_b.fasta")
+
+
+def test_cycle_alignment(inp_fasta):
+    """Test cycle_alignment function."""
+    list_of_seqs = SeqIO.parse(open(inp_fasta), "fasta")
+    ref_seq = "MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET"
+    max_id_chain, max_id = cycle_alignment(list_of_seqs, ref_seq, "aln")
+    aln_content = open("aln", "r").read()
+    assert max_id_chain == "B"
+    assert max_id == 1.0
+    first_line = aln_content.split(os.linesep)[0]
+    exp_first_line = f"target            0 {ref_seq}"
+    assert first_line == exp_first_line
+    os.remove("aln")