def test_split_strands_se_2():
test_bam = 'bam/se_unsplit_2.bam'
test_fwd = 'bam/se_split_2_fwd.bam'
test_rev = 'bam/se_split_2_rev.bam'
reverse = False
ss.split_strands(test_bam,test_fwd,test_rev, reverse)
fwd_handle = pysam.AlignmentFile(test_fwd)
rev_handle = pysam.AlignmentFile(test_rev)
for read in fwd_handle:
assert (read.is_reverse == False)
for read in rev_handle:
assert (read.is_reverse == True)
fwd_handle.close()
rev_handle.close()
def test_split_strands_pe_1():
test_bam = 'bam/pe_unsplit_1.bam'
test_fwd = 'bam/pe_split_1_fwd.bam'
test_rev = 'bam/pe_split_1_rev.bam'
reverse = True
ss.split_strands(test_bam,test_fwd,test_rev, reverse)
fwd_handle = pysam.AlignmentFile(test_fwd)
rev_handle = pysam.AlignmentFile(test_rev)
for read in rev_handle:
assert ((read.is_reverse == False and read.is_read1) or
(read.is_reverse == True and read.is_read2))
for read in fwd_handle:
assert ((read.is_reverse == True and read.is_read1) or
(read.is_reverse == False and read.is_read2))
fwd_handle.close()
rev_handle.close()