Add test case for checking RankScore is float in processed VCF

Going forward, the expected behavior is that RankScore
is to be a float-type value in VCFs.

Signed-off-by: Tor Björgen <[email protected]>

tests/functionality/test_score_variants_ranks_score_is_float.py

@@ -0,0 +1,143 @@
+import pytest
+from tempfile import NamedTemporaryFile
+from typing import Dict, Union
+from click.testing import CliRunner
+
+from genmod.commands import score_command, score_compounds_command
+from genmod.vcf_tools import HeaderParser, get_variant_dict, get_info_dict
+
+ANNOTATED_VCF_FILE = "tests/fixtures/test_vcf_annotated.vcf"
+SCORE_CONFIG = "tests/fixtures/score_variants/genmod_example.ini"
+
+
+def _parse_variant_file(file_path: str) -> HeaderParser:
+    """
+    Parse VCF header fields
+    :param file_path: VCF to be read
+    :raises ValueError: in case file is empty
+    """
+    with open(file_path, 'r') as variant_file:
+        head = HeaderParser()
+        for line_index, line in enumerate(variant_file):
+            line = line.rstrip()
+            if line.startswith('#'):
+                if line.startswith('##'):
+                    head.parse_meta_data(line)
+                else:
+                    head.parse_header_line(line)
+            else:
+                break
+        if line_index == 0:
+            raise ValueError('Expected contents in file, got none')
+    return head
+
+
+def _generate_variants_from_file(file_path: str) -> Dict[str, Union[str, int, float]]:
+    """
+    Yield variants from VCF file.
+    :param file_path: VCF to be read
+    """
+    header = _parse_variant_file(file_path=file_path)
+    with open(file_path, 'r') as variant_file:
+        for line in variant_file:
+            if line.startswith('#'):
+                continue
+            variant: Dict[str, str] = get_variant_dict(line, header.header)
+            variant['info_dict'] = get_info_dict(variant['INFO'])
+            yield variant
+
+
+def _generate_rank_score_strings_from_file(file_path: str) -> str:
+    """
+    Yield rank score strings from VCF.
+    :param file_path: VCF to be read
+    """
+    for variant in _generate_variants_from_file(file_path=file_path):
+        rank_score_entry: str = variant['info_dict'].get('RankScore', '')
+        for family_rank_score in rank_score_entry.split(','):
+            family_rank_score = family_rank_score.split(':')
+            family_id: str = family_rank_score[0]
+            rank_score: str = family_rank_score[1]
+            yield rank_score
+
+
+def _check_rankscore_string_is_float(rank_score_string: str):
+    """
+    Check to see if a rank score string contains a floating point value.
+    :param rank_score_string: A string to be checked
+    :raises AssertionError: In case rank_score_string is not a float-type value
+    """
+    # Check decimal point presence
+    assert '.' in rank_score_string
+    # Check all numerical digits, might contain period and minus sign.
+    assert rank_score_string \
+        .replace('.', '') \
+        .replace('-','') \
+        .isdigit()
+    # Check successfully parsed to float
+    assert isinstance(float(rank_score_string), float)
+
+
+def test_check_rankscore_string_is_float():
+    """
+    Test for checking integrity of rank score float check method.
+    """
+    # GIVEN some rank score strings
+    # WHEN running the method under test
+    # THEN expect it to behave as expected in positive case
+    _check_rankscore_string_is_float('0.0')
+    _check_rankscore_string_is_float('132.1')
+    _check_rankscore_string_is_float('132.10')
+    _check_rankscore_string_is_float('-10.0')
+
+    # THEN expect it to behave as expected in negative case
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('')
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('132')
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('b')
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('0')
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('.')
+    with pytest.raises(AssertionError):
+        _check_rankscore_string_is_float('-')
+
+
+def test_rankscore_is_float_type():
+    """
+    Test to make sure RankScore value is float
+    provided by both the CLI command 'score' and 'compound'.
+    """
+    # GIVEN some VCF file to be ranked
+    runner = CliRunner()
+    # WHEN computing rank score
+    result = runner.invoke(score_command, [
+        ANNOTATED_VCF_FILE,
+        '-c',
+        SCORE_CONFIG
+        ]
+    )
+    assert result.exit_code == 0
+    temporary_file = NamedTemporaryFile()
+    with open(temporary_file.name, 'w') as file:
+        file.write(result.stdout_bytes.decode('utf-8'))  # Save processed VCF to file
+    # THEN expect all rank scores to be float type
+    for rank_score_string in _generate_rank_score_strings_from_file(file_path=temporary_file.name):
+        _check_rankscore_string_is_float(rank_score_string)
+
+    # GIVEN some ranked VCF file, run compound scoring (which modify the RankScore)
+    runner = CliRunner()
+    # WHEN computing compound score
+    result = runner.invoke(score_compounds_command, [
+        temporary_file.name,
+        ]
+    )
+    assert result.exit_code == 0
+    temporary_file = NamedTemporaryFile()
+    with open(temporary_file.name, 'w') as file:
+        file.write(result.stdout_bytes.decode('utf-8'))  # Save processed VCF to file
+    # THEN expect all rank scores (including modified compound scores) to be float type
+    for rank_score_string in _generate_rank_score_strings_from_file(file_path=temporary_file.name):
+        _check_rankscore_string_is_float(rank_score_string)