def test_external_add_nh_flag(self):
with execution(None) as ex:
f = external_add_nh_flag(ex, os.path.join(path, "mapped.sam"))
g = add_nh_flag(os.path.join(path, "mapped.sam"))
m = md5sum(ex, f)
m2 = md5sum(ex, g)
self.assertEqual(m, m2)
def test_parallel_bowtie_lsf(self):
with execution(None) as ex:
bam = parallel_bowtie(
ex, os.path.join(path, "selected_transcripts"), os.path.join(path, "reads.raw"), n_lines=250, via="lsf"
)
sam = bam_to_sam(ex, bam)
new_sam = remove_lines_matching(ex, "@PG", sam)
new_bam = sam_to_bam(ex, new_sam)
m = md5sum(ex, new_bam)
self.assertEqual(m, "find right md5sum")
def test_parallel_bowtie_local(self):
with execution(None) as ex:
bam = parallel_bowtie(
ex,
os.path.join(path, "selected_transcripts"),
os.path.join(path, "reads.raw"),
n_lines=250,
via="local",
)
sam = bam_to_sam(ex, bam)
new_sam = remove_lines_matching(ex, "@PG", sam)
new_bam = sam_to_bam(ex, new_sam)
self.assertEqual(md5sum(ex, new_bam), "2e6bd8ce814949075715b8ffddd1dcd5")
def test_parallel_bowtie_local_with_nh_flags(self):
with execution(None) as ex:
bam = parallel_bowtie(
ex,
os.path.join(path, "selected_transcripts"),
os.path.join(path, "reads.raw"),
n_lines=250,
add_nh_flags=True,
via="local",
)
sam = bam_to_sam(ex, bam)
new_sam = remove_lines_matching(ex, "@PG", sam)
new_bam = sam_to_bam(ex, new_sam)
self.assertEqual(md5sum(ex, new_bam), "529cd218ec0a35d5d0a23fd7b842ee20")
def test_parallel_bowtie_lsf_with_nh_flags(self):
with execution(None) as ex:
bam = parallel_bowtie(
ex,
os.path.join(path, "selected_transcripts"),
os.path.join(path, "reads.raw"),
n_lines=250,
add_nh_flags=True,
via="lsf",
)
sam = bam_to_sam(ex, bam)
new_sam = remove_lines_matching(ex, "@PG", sam)
new_bam = sam_to_bam(ex, new_sam)
m = md5sum(ex, new_bam)
self.assertEqual(m, "7b7c270a3980492e82591a785d87538f")
def test_internal_add_nh_flag(self):
with execution(None) as ex:
f = add_nh_flag(os.path.join(path, "mapped.sam"))
m = md5sum(ex, f)
self.assertEqual(m, "50798b19517575533b8ccae5b1369a3e")