Added tests for parse_gbk class

tests/test_gbk.py

@@ -0,0 +1,72 @@
+import pytest
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+from Bio.Seq import Seq
+import gzip
+from locidex.classes.gbk import parse_gbk
+
+# Helper to create a GenBank file
+def create_genbank_file(path, seq_records, compress=False):
+    mode = 'wt'
+    _open = gzip.open if compress else open
+    with _open(path, mode) as f:
+        for record in seq_records:
+            # Ensure the record includes necessary annotations for GenBank
+            record.annotations["molecule_type"] = "DNA"
+        SeqIO.write(seq_records, f, "genbank")
+
+@pytest.fixture
+def genbank_file(tmp_path):
+    # Create a GenBank file for testing
+    file_path = tmp_path / "test.gbk"
+    seqs = [SeqRecord(Seq("ATGGAATAG"), id="test_seq1", description="A simple sequence", annotations={"molecule_type": "DNA"})]
+    create_genbank_file(file_path, seqs)
+    return file_path
+
+@pytest.fixture
+def gzip_genbank_file(tmp_path):
+    # Create a gzip-compressed GenBank file
+    file_path = tmp_path / "test_compressed.gbk.gz"
+    seqs = [SeqRecord(Seq("ATGGAATAG"), id="test_seq1", description="A simple sequence", annotations={"molecule_type": "DNA"})]
+    create_genbank_file(file_path, seqs, compress=True)
+    return file_path
+
+def test_initialization_nonexistent_file():
+    # Ensure it handles non-existent files correctly
+    with pytest.raises(FileNotFoundError):
+        parse_gbk("nonexistent.gbk")
+
+def test_initialization_existing_file(genbank_file):
+    # Test initialization with an existing file
+    parser = parse_gbk(str(genbank_file))
+    assert parser.status, "Parser should be successfully initialized with a valid file"
+
+def test_parse_reference_gbk(genbank_file):
+    # Test the parsing functionality
+    parser = parse_gbk(str(genbank_file))
+    parser.parse_reference_gbk()
+    assert len(parser.seq_obj) > 0, "Should parse GenBank file and store data"
+
+def test_get_acs(genbank_file):
+    # Test getting accession numbers
+    parser = parse_gbk(str(genbank_file))
+    acs = parser.get_acs()
+    assert len(acs) > 0, "Should return list of accession numbers"
+
+def test_get_seq_by_acs(genbank_file):
+    # Test fetching sequences by accession number
+    parser = parse_gbk(str(genbank_file))
+    seq_data = parser.get_seq_by_acs('test_seq1')
+    assert seq_data, "Should return sequence data for given accession"
+
+def test_get_feature(genbank_file):
+    # Test fetching features by accession
+    parser = parse_gbk(str(genbank_file))
+    feature_data = parser.get_feature('test_seq1', 'source')
+    assert feature_data, "Should return specific feature data for given accession"
+
+def test_gene_prediction_gzip_fasta(gzip_genbank_file):
+    # Ensure it can handle gzip compressed files
+    parser = parse_gbk(str(gzip_genbank_file))
+    assert parser.status, "Should be able to handle gzip compressed GenBank files"
+    assert len(parser.seq_obj) > 0, "Should parse compressed GenBank file and store data"