def test_sj_02(self):
test_id = 'splice_site_motif_02'
input_sam = TEST_DIR + "test_" + test_id + ".in.sam"
input_bam = T_TEST_DIR + "test_" + test_id + ".fixed.bam"
input_file = T_TEST_DIR + "test_" + test_id + ".dbed"
gtf_file = None
fasta_file = TEST_DIR + "test_" + test_id + ".in.fa"
output_file = T_TEST_DIR + "test_" + test_id + ".out.dbed"
test_file = TEST_DIR + "test_" + test_id + ".out.dbed"
# sam -> fixed bam
sam_to_fixed_bam(input_sam, input_bam, T_TEST_DIR)
# fixed bam -> dr-disco detect
ic = IntronDecomposition(input_bam)
ic.decompose(0)
fh = open(input_file, "w")
ic.export(fh)
fh.close()
# dr-disco-detect (skip classify) -> dr-disco integrate
cl = DetectOutput(input_file)
cl.integrate(output_file, gtf_file, fasta_file)
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_sj_04__CA_GT_d4(self):
test_id = 'splice_site_motif_04'
input_sam = TEST_DIR + "test_" + test_id + ".in.sam"
input_bam = T_TEST_DIR + "test_" + test_id + ".fixed.bam"
input_file = T_TEST_DIR + "test_" + test_id + ".dbed"
gtf_file = None
fasta_file = TEST_DIR + "test_" + test_id + ".in.fa"
output_file = T_TEST_DIR + "test_" + test_id + ".out.dbed"
test_file = TEST_DIR + "test_" + test_id + ".out.dbed"
# sam -> fixed bam
sam_to_fixed_bam(input_sam, input_bam, T_TEST_DIR)
# fixed bam -> dr-disco detect
ic = IntronDecomposition(input_bam)
ic.decompose(0)
fh = open(input_file, "w")
ic.export(fh)
fh.close()
# dr-disco-detect (skip classify) -> dr-disco integrate
cl = DetectOutput(input_file)
# originally, this triggered an exception, now we just log an error
# cl.integrate(output_file, gtf_file, fasta_file)
# self.assertRaises(Exception, cl.integrate, output_file, gtf_file, fasta_file)
cl.integrate(output_file, gtf_file, fasta_file)
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_s041_nocrash(self):
test_id = 'terg_s041_b'
input_file = TEST_DIR + "test_" + test_id + ".in.dbed"
gtf_file = TEST_DIR + "example_refseq.gff"
test_file = TEST_DIR + "test_" + test_id + ".out.txt"
output_file = T_TEST_DIR + "test_" + test_id + ".out.txt"
cl = DetectOutput(input_file)
cl.integrate(output_file, gtf_file, None)
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_s041_no_gtf(self):
test_id = 'terg_s041_b'
input_file = TEST_DIR + "test_" + test_id + ".in.dbed"
gtf_file = None
test_file = TEST_DIR + "test_" + test_id + ".out.txt"
output_file = T_TEST_DIR + "test_" + test_id + ".out.txt"
cl = DetectOutput(input_file)
cl.integrate(output_file, gtf_file, None)
#self.assertTrue(filecmp.cmp(test_file, output_file), msg="diff '" + test_file + "' '" + output_file + "':\n" + subprocess.Popen(['diff', test_file, output_file], stdout=subprocess.PIPE).stdout.read())
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_s041(self):
test_id = 'terg_s041'
input_file = TEST_DIR + "test_" + test_id + ".in.dbed"
gtf_files = [
TEST_DIR + "test_" + test_id + ".in.gtf",
TEST_DIR + "test_" + test_id + ".in.no_chr_prefix.gtf"
]
test_file = TEST_DIR + "test_" + test_id + ".out.txt"
output_file = T_TEST_DIR + "test_" + test_id + ".out.txt"
for gtf_file in gtf_files:
cl = DetectOutput(input_file)
cl.integrate(output_file, gtf_file, None)
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_in_frame_non_hybrid_protein(self):
test_id = 'in_frame_non_hybrid_protein'
# Transcript ID's necessary:
# - TMPRSS2: ENST00000424093
# - ERG: ENST00000398910
input_file = TEST_DIR + "test_" + test_id + ".in.dbed"
gtf_files = [TEST_DIR + "test_" + test_id + ".gtf"]
test_file = TEST_DIR + "test_" + test_id + ".out.txt"
output_file = T_TEST_DIR + "test_" + test_id + ".out.txt"
for gtf_file in gtf_files:
cl = DetectOutput(input_file)
cl.integrate(output_file, gtf_file, None)
#self.assertTrue(filecmp.cmp(test_file, output_file), msg="diff '" + test_file + "' '" + output_file + "':\n" + subprocess.Popen(['diff', test_file, output_file], stdout=subprocess.PIPE).stdout.read())
self.assertTrue(filecmp.cmp(test_file, output_file),
msg=get_diff(test_file, output_file))
def test_01(self):
test_id = '01'
unfixed_sam = TEST_DIR + "test_" + test_id + ".sam"
fixed_bam = T_TEST_DIR + "test_" + test_id + ".fixed.bam"
drdisco_detect = T_TEST_DIR + "test_" + test_id + "_detect.out.txt"
drdisco_detect_test = TEST_DIR + "test_" + test_id + "_detect.out.txt"
drdisco_classify = T_TEST_DIR + "test_" + test_id + "_classify.out.txt"
drdisco_classify_test = TEST_DIR + "test_" + test_id + "_classify.out.txt"
drdisco_integrate = T_TEST_DIR + "test_" + test_id + "_integrate.out.txt"
drdisco_integrate_test = TEST_DIR + "test_" + test_id + "_integrate.out.txt"
# Step 01: dr-disco fix (don't check please)
sam_to_fixed_bam(unfixed_sam, fixed_bam, T_TEST_DIR)
# Step 02: dr-disco detect (check appropriate values and columns)
ic = IntronDecomposition(fixed_bam)
ic.decompose(0)
with open(drdisco_detect, "w") as fh:
ic.export(fh)
self.assertTrue(filecmp.cmp(drdisco_detect_test, drdisco_detect), msg=get_diff( drdisco_detect_test , drdisco_detect ))
# Step 03: dr-disco classify
cl = DetectOutput(drdisco_detect)
cl.classify(drdisco_classify, False, Blacklist(), 25, True)
self.assertTrue(filecmp.cmp(drdisco_classify_test, drdisco_classify), msg=get_diff( drdisco_classify_test , drdisco_classify ))
# Step 04: dr-disco integrate
cl = DetectOutput(drdisco_classify)
cl.integrate(drdisco_integrate, None, None)
self.assertTrue(filecmp.cmp(drdisco_integrate_test, drdisco_integrate), msg=get_diff( drdisco_integrate_test , drdisco_integrate ))