def test_readsHeaderFromBamFile1Correctly(self):
bf = BamFile('Tests/Bam/bam1.bam')
bf.readHeader(bf.generator())
assert bf.file_chromosomes != []
def test_getBamRecordsFromInvalidBamFileThrows(self):
bf = BamFile('Tests/Bam/ex1.bam')
with pytest.raises(PybamWarn):
for _ in bf.getBamRecords():
print('help!')
def test_getFileChromosomesFromFile2Correctly(self):
bf = BamFile('Tests/Bam/bam2.bam')
for sequence in bf.getBamRecords():
assert sequence.sam_rname(
bf.file_chromosomes) == '*' or sequence.sam_rname(
bf.file_chromosomes).decode("utf-8") == '1'
def test_getFirstSequenceFromFile2Correctly(self):
bf = BamFile('Tests/Bam/bam2.bam')
records = bf.getBamRecords()
record = next(records)
# the known value of the first sequence
assert record.sam_seq == 'GTTGTTTCTTCCTTTTTTCCCCTCTTCCCCTTCCTGTCTTGTGTTTTTTCTGAACCCCACATCTGCCATCATTTCTCTCCTCTAGAGTCCCTTGCTTCTGC'
def test_getBamRecordsFromBamFile2Correctly(self):
bf = BamFile('Tests/Bam/bam2.bam')
for sequence in bf.getBamRecords():
assert sequence.bam_qname.decode("utf-8").startswith(
'HWI-1KL120:88:D0LRBACXX:1:1101:')
def test_getFirstSequenceFromFile1Correctly(self):
bf = BamFile('Tests/Bam/bam1.bam')
records = bf.getBamRecords()
record = next(records)
# the known value of the first sequence
assert record.sam_seq == 'GAGAGGTCAGCGTGAGCCCCTTGCCTCACACCGGCCCCTCTCACGCCGAGAGAGGTCAGCGTGAGCCCCTTGCCTCACACCGGCCCCTCCCACGCCGAGAG'