samtools_mcp

#!/usr/bin/env python3 """ Test file for Samtools MCP Server. This file tests the functionality of the samtools_mcp module. """ import os import unittest import tempfile import samtools_mcp class TestSamtoolsMCP(unittest.TestCase): """Test cases for Samtools MCP.""" def setUp(self): """Set up test environment.""" self.test_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "bam") self.test1_bam = os.path.join(self.test_dir, "test1.bam") self.test2_bam = os.path.join(self.test_dir, "test2.bam") # Make sure the test files exist self.assertTrue(os.path.exists(self.test1_bam), f"Test file {self.test1_bam} does not exist") self.assertTrue(os.path.exists(self.test2_bam), f"Test file {self.test2_bam} does not exist") def test_view_count(self): """Test samtools view with count option.""" # Test the view count for test1.bam result = samtools_mcp.samtools_view(self.test1_bam, count_only=True) self.assertEqual(result.strip(), "15", f"Expected 15 reads in {self.test1_bam}, got {result}") # Test the view count for test2.bam result = samtools_mcp.samtools_view(self.test2_bam, count_only=True) self.assertEqual(result.strip(), "12", f"Expected 12 reads in {self.test2_bam}, got {result}") def test_flagstat(self): """Test samtools flagstat.""" # Test flagstat on test1.bam result = samtools_mcp.samtools_flagstat(self.test1_bam) self.assertIn("15 + 0 in total", result, "Expected 15 reads in flagstat output") self.assertIn("4 + 0 paired in sequencing", result, "Expected 4 paired reads in flagstat output") # Test flagstat on test2.bam result = samtools_mcp.samtools_flagstat(self.test2_bam) self.assertIn("12 + 0 in total", result, "Expected 12 reads in flagstat output") self.assertIn("2 + 0 paired in sequencing", result, "Expected 2 paired reads in flagstat output") def test_header_view(self): """Test viewing the header of a BAM file.""" result = samtools_mcp.samtools_view(self.test1_bam, header_only=True) self.assertIn("@HD", result, "Expected @HD in header") self.assertIn("@SQ", result, "Expected @SQ in header") def test_view_with_flags(self): """Test view with flag filtering.""" # Get only paired reads (flag 0x1) result = samtools_mcp.samtools_view(self.test1_bam, flags_required="1") lines = [line for line in result.split('\n') if line.strip()] self.assertEqual(len(lines), 4, f"Expected 4 paired reads, got {len(lines)}") def test_sort_and_index(self): """Test sorting and indexing a BAM file.""" with tempfile.TemporaryDirectory() as tmpdir: sorted_bam = os.path.join(tmpdir, "test1.sorted.bam") # Sort the BAM file sort_result = samtools_mcp.samtools_sort(self.test1_bam, output_file=sorted_bam) self.assertTrue(os.path.exists(sorted_bam), f"Sorted BAM file {sorted_bam} was not created") # Index the sorted BAM file index_result = samtools_mcp.samtools_index(sorted_bam) self.assertTrue(os.path.exists(sorted_bam + ".bai"), "BAM index file was not created") def test_version(self): """Test getting samtools version.""" version = samtools_mcp.get_samtools_version() self.assertIn("samtools", version.lower(), "Expected 'samtools' in version string") self.assertIn("htslib", version.lower(), "Expected 'htslib' in version string") def test_help(self): """Test getting help information.""" help_text = samtools_mcp.get_samtools_help() self.assertIn("usage", help_text.lower(), "Expected 'usage' in help text") # Test command-specific help view_help = samtools_mcp.get_command_help("view") self.assertIn("view", view_help.lower(), "Expected 'view' in view help text") def test_list_files(self): """Test listing BAM files.""" result = samtools_mcp.samtools_list_files(self.test_dir) self.assertIn("test1.bam", result, "Expected test1.bam in file listing") self.assertIn("test2.bam", result, "Expected test2.bam in file listing") if __name__ == "__main__": unittest.main()