From 7e7ff8f868ad1bc5cb5274bce97cab9657153dd3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=BCck?= <m991k@b260-pc003.inet.dkfz-heidelberg.de>
Date: Wed, 8 May 2024 10:51:45 +0200
Subject: [PATCH] added test for calculate_allele frequencies

---
 deeprvat/annotations/annotations.py           |   9 ++-
 tests/annotations/test_annotations.py         |  68 ++++++++++++++++++
 .../expected/af_df.parquet                    | Bin 0 -> 2313 bytes
 .../input/genotypes.h5                        | Bin 0 -> 6924 bytes
 .../input/variants.parquet                    | Bin 0 -> 3522 bytes
 5 files changed, 76 insertions(+), 1 deletion(-)
 create mode 100644 tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/expected/af_df.parquet
 create mode 100644 tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/input/genotypes.h5
 create mode 100644 tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/input/variants.parquet

diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py
index 72eba673..e31016cc 100644
--- a/deeprvat/annotations/annotations.py
+++ b/deeprvat/annotations/annotations.py
@@ -1738,7 +1738,14 @@ def process_vep(
     )
     if "#Uploaded_variation" in vep_file.columns:
         vep_file = vep_file.merge(vcf_df, on="#Uploaded_variation", how = 'left')
-        vep_file.loc[vep_file.chrom.isna(),['chrom','pos','ref','alt']]=vep_file[vep_file['chrom'].isna()]['#Uploaded_variation'].str.replace("_", ":").str.replace("/", ":").str.split(':', expand=True).values
+        if vep_file.chrom.isna().sum()>0:
+            vep_file.loc[vep_file.chrom.isna(),['chrom','pos','ref','alt']]=vep_file[vep_file['chrom'].isna()]['#Uploaded_variation'].str.replace("_", ":").str.replace("/", ":").str.split(':', expand=True).values
+    assert vep_file.chrom.isna().sum() == 0
+    assert vep_file.pos.isna().sum() == 0
+    assert vep_file.ref.isna().sum() == 0
+    assert vep_file.alt.isna().sum() == 0
+    
+    
     if "pos" in vep_file.columns:
         vep_file["pos"] = vep_file["pos"].astype(int)
 
diff --git a/tests/annotations/test_annotations.py b/tests/annotations/test_annotations.py
index 83ae128e..962ca10d 100644
--- a/tests/annotations/test_annotations.py
+++ b/tests/annotations/test_annotations.py
@@ -372,6 +372,74 @@ def test_merge_absplice_scores(
     assert written_results.shape == expected_results.shape
     assert_frame_equal(written_results, expected_results, check_exact = False)
 
+@pytest.mark.parametrize(
+    "test_data_name_dir, genotype_file, variant_file, expected",
+    [
+        (   "calculate_allele_frequency_small",
+            "genotypes.h5",
+            "variants.parquet",
+            "af_df.parquet",
+        ),
+    ]
+)
+def test_calculate_allele_frequencies(
+     test_data_name_dir, genotype_file, variant_file, expected, tmp_path
+):
+    current_test_data_dir = tests_data_dir / 'calculate_allele_frequency' / test_data_name_dir
+    genotype_filepath = current_test_data_dir / 'input' /  genotype_file
+    variant_filepath = current_test_data_dir / 'input' /variant_file
+    expected_path = current_test_data_dir / 'expected' / expected
+    output_path = tmp_path / 'out.parquet'
+    cli_runner = CliRunner()
+    cli_parameters = [
+        'get-af-from-gt',
+        genotype_filepath.as_posix(),
+        variant_filepath.as_posix(),
+        output_path.as_posix(),
+        ]
+    result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False)
+    assert result.exit_code == 0
+    written_results = pd.read_parquet(output_path)
+    expected_results = pd.read_parquet(expected_path)
+    assert written_results.shape == expected_results.shape
+    assert_frame_equal(written_results, expected_results[written_results.columns], check_exact = False)
+
+
+
+
+# @pytest.mark.parametrize(
+#     "test_data_name_dir, input_file_1, input_file_2, parameter1, expected",
+#     [
+#         (   "test_name_dir",
+#             "input_file1.parquet",
+#             "input_file2.parquet",
+#             "8",
+#             "expected.parquet",
+#         ),
+#     ]
+# )
+# def template(
+#      test_data_name_dir, input_file_1, input_file_2, parameter1, expected, tmp_path
+# ):
+#     current_test_data_dir = tests_data_dir / 'test_name' / test_data_name_dir
+#     input_path1 = current_test_data_dir / 'input' /  input_file_1
+#     input_path2 = current_test_data_dir / 'input' /input_file_2
+#     expected_path = current_test_data_dir / 'expected' / expected
+#     output_path = tmp_path / 'out.parquet'
+#     cli_runner = CliRunner()
+#     cli_parameters = [
+#         'function-name',
+#         input_path1.as_posix(),
+#         input_path2.as_posix(),
+#         output_path.as_posix(),
+#         parameter1,
+#         ]
+#     result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False)
+#     assert result.exit_code == 0
+#     written_results = pd.read_parquet(output_path)
+#     expected_results = pd.read_parquet(expected_path)
+#     assert written_results.shape == expected_results.shape
+#     assert_frame_equal(written_results, expected_results[written_results.columns], check_exact = False)
 
 # @pytest.mark.parametrize(
 #     "test_name_dir, input_file_1, input_file_2, parameter1, expected",
diff --git a/tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/expected/af_df.parquet b/tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/expected/af_df.parquet
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diff --git a/tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/input/genotypes.h5 b/tests/annotations/test_data/calculate_allele_frequency/calculate_allele_frequency_small/input/genotypes.h5
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