
import unittest
import user_code
import ast
import re   
import importlib
import csv
import unittest
import importlib

class TestTask(unittest.TestCase):
    def test_mixed_alignment(self):
        import user_code
        importlib.reload(user_code)
        func = getattr(user_code, 'score_alignment', None)
        _dynamic_test(
            self,
            callable(func),
            "score_alignment function exists",
            "score_alignment function is not defined"
        )
        result = func("ATG-C", "AT-AC") if func else None
        _dynamic_test(
            self,
            result is not None and result == (3, 0, 2),
            "Correct counts for mixed alignment (ATG-C, AT-AC)",
            f"Expected (3, 0, 2), got {result}"
        )

    def test_gaps_counted(self):
        import user_code
        importlib.reload(user_code)
        func = getattr(user_code, 'score_alignment', None)
        result = func("A--GC", "ATAGC") if func else None
        _dynamic_test(
            self,
            result is not None and result == (3, 0, 2),
            "Correctly counts gaps in alignment (A--GC, ATAGC)",
            f"Expected (3, 0, 2), got {result}"
        )

    def test_empty_sequences(self):
        import user_code
        importlib.reload(user_code)
        func = getattr(user_code, 'score_alignment', None)
        result = func("", "") if func else None
        _dynamic_test(
            self,
            result is not None and result == (0, 0, 0),
            "Returns (0, 0, 0) for empty sequences",
            f"Expected (0, 0, 0), got {result}"
        )

    def test_all_mismatches(self):
        import user_code
        importlib.reload(user_code)
        func = getattr(user_code, 'score_alignment', None)
        result = func("ACGT", "TGCA") if func else None
        _dynamic_test(
            self,
            result is not None and result == (0, 4, 0),
            "Returns all mismatches if no positions match and no gaps",
            f"Expected (0, 4, 0), got {result}"
        )

    def test_all_matches(self):
        import user_code
        importlib.reload(user_code)
        func = getattr(user_code, 'score_alignment', None)
        result = func("AGCT", "AGCT") if func else None
        _dynamic_test(
            self,
            result is not None and result == (4, 0, 0),
            "Returns all matches if all positions match and no gaps",
            f"Expected (4, 0, 0), got {result}"
        )

def _dynamic_test(test_case, condition, success_message, failure_message):
    if condition:
        test_case._testMethodName = success_message
        test_case.assertTrue(True, success_message)
    else:
        test_case._testMethodName = failure_message
        test_case.fail(failure_message)

def normalize_text(text):
    text = text.lower()
    text = re.sub(r"\\s{2,}", " ", text)
    text = re.sub(r"\\s*([,:?])\\s*", r"\\1 ", text)
    return text.strip()

def change_var(code: str, var_name: str, value: str) -> str:
    tree = ast.parse(code)
    lines = code.splitlines()
    changed = False
    # Collect all assignment nodes to modify
    assign_nodes = [
        (i, node)
        for i, node in enumerate(tree.body)
        if isinstance(node, ast.Assign)
        and any(isinstance(target, ast.Name) and target.id == var_name for target in node.targets)
    ]

    # If nothing to change, return unmodified code
    if not assign_nodes:
        return code

    # Perform replacements for all matching assignments (from last to first to not break line offsets)
    for i, node in reversed(assign_nodes):
        start_line = node.lineno - 1
        line = lines[start_line]
        indent = ' ' * (len(line) - len(line.lstrip()))
        lines[start_line] = f"{indent}{var_name} = {value}"
        next_line = len(lines)
        for next_node in tree.body[i+1:]:
            if hasattr(next_node, 'lineno'):
                next_line = next_node.lineno - 1
                break
        if next_line > start_line + 1:
            lines[start_line+1:next_line] = []
        changed = True

    return '\\n'.join(lines) if changed else code

if __name__ == "__main__":
    unittest.main()


test_main.py

A beginner-friendly course introducing Python programming through real-world bioinformatics problems. Learn to handle biological data formats, analyze DNA sequences, process next-generation sequencing data, and build reproducible analysis pipelines—all with engaging, hands-on tasks and clear explanations.

Dive into sequence analysis techniques, including alignment basics and motif searching, to uncover biological insights from DNA and protein sequences.

Learn how to process next-generation sequencing (NGS) data, including read quality analysis and coverage calculations, using Python.

Explore gene expression analysis using RNA-seq data and learn how to build reproducible bioinformatics workflows with Python.

Challenge: Score Sequence Alignments

Solution

Challenge: Score Sequence Alignments

Solution