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