def test_left_span_4():
print("Tests a single read with a single junction N")
print("Region: chr10:122666367-122668067:+")
print("Read: D80KHJN1:241:C5HF7ACXX:6:2113:6890:67612")
print("Should support skipping (read spans this region(intron)")
bam = single_jxn_skip_4()
jxc_coord = 'chr10:122666367-122668067:+'
min_overlap = 8
aligned_file = pysam.AlignmentFile(bam, "rb")
chrom, five, three, strand = j.parse_jxn_string(jxc_coord)
for read in aligned_file.fetch(chrom, five - min_overlap, five):
skip, incl = j.left_span(read, three, min_overlap)
assert skip == False
assert incl == False
def test_left_span_1():
print("Tests a single read with a single junction N")
print("Region: chr10:135209281-135209666:+")
print("Read: D80KHJN1:241:C5HF7ACXX:6:1307:9279:87799")
print("Should support skipping (read spans this region(intron)")
bam = single_jxn_skip_1()
jxc_coord = 'chr10:135209281-135209666:+'
min_overlap = 1
aligned_file = pysam.AlignmentFile(bam, "rb")
chrom, five, three, strand = j.parse_jxn_string(jxc_coord)
for read in aligned_file.fetch(chrom, five - min_overlap, five):
skip, incl = j.left_span(read, three, min_overlap)
assert skip == True
assert incl == False
def test_right_span_inclusion_7():
print("Tests a inclusion read that doesn't quite overlap over "
"the min_overlap reqs")
print("Region: chr10:122666367-122668067:+")
print("Read: D80KHJN1:241:C5HF7ACXX:6:2113:2908:58516")
print("Should support nothing (would support inclusion "
"if min overhang wasn't 34")
bam = inclusion_7()
min_overlap = 34
jxc_coord = 'chr10:122666367-122668067:+'
aligned_file = pysam.AlignmentFile(bam, "rb")
chrom, five, three, strand = j.parse_jxn_string(jxc_coord)
for read in aligned_file.fetch(chrom, five - min_overlap, five):
skip, incl = j.right_span(read, five, min_overlap)
assert skip == False
assert incl == False