def test_BamFile_setup(): test_header3 = bam.BamFile(os.path.join(dir, "header2.bam"), "samtools", no_initial_index=False) assert test_header3.filepath == os.path.join(dir, "header2.bam") assert test_header3.is_indexed() is True
def test_BamFile(): test_header = bam.BamFile(os.path.join(dir, "header.bam"), "samtools", no_initial_index=True) test_header2 = bam.BamFile(os.path.join(dir, "header2.bam"), "samtools", no_initial_index=True) test_header3 = bam.BamFile(os.path.join(dir, "tinyheader2.bam"), "samtools", no_initial_index=True) assert test_header.filepath == os.path.join(dir, "header.bam") assert test_header2.filepath == os.path.join(dir, "header2.bam") assert test_header3.filepath == os.path.join(dir, "tinyheader2.bam") os.utime(os.path.join(dir, "header.bam.bai"), None) assert test_header.is_indexed() is True assert test_header2.is_indexed() is False os.utime(os.path.join(dir, "tinyheader2.bai"), None) assert test_header3.is_indexed() is True
def test_check_bam_fasta_compatibility(): test_bam = bam.BamFile(os.path.join(dir, "toy.bam"), "samtools", no_initial_index=True) test2_bam = bam.BamFile(os.path.join(dir, "tinyheader.bam"), "samtools", no_initial_index=True) test_fasta = reftools.RefFasta(os.path.join(dir, "toy.fasta"), "samtools", "bwa", no_initial_index=True) test2_fasta = reftools.RefFasta(os.path.join(dir, "toy3.fasta"), "samtools", "bwa", no_initial_index=True) assert utils.check_bam_fasta_compatibility(test_bam, test_fasta) is True assert utils.check_bam_fasta_compatibility(test2_bam, test_fasta) is False assert utils.check_bam_fasta_compatibility(test_bam, test2_fasta) is False