def test_paired_pairBedFile(self):
refbedfile = os.path.join(referencedir, 'pairBedFile.bed')
resbedfile = os.path.join(resultdir, 'pairBedFile.bed')
self.test_case('example_paired.bam', 'example_paired.paired.sam', '--paired --minId=0 --minCover=0 --pairBedFile=' + resbedfile)
if TestFilterBam.opt_compare:
aug_assertions.assertEqualFiles(self, refbedfile, resbedfile, TestFilterBam.opt_html, htmldir)
os.remove(resbedfile)
def test_compare(self, refsamfile, resbamfile, ressamfile):
os.chdir(default_wd)
# compare results
if TestFilterBam.opt_compare:
aug_assertions.assertEqualFiles(self, refsamfile, ressamfile, TestFilterBam.opt_html, htmldir)
os.remove(resbamfile)
os.remove(ressamfile)
def test_commonGeneFile(self):
reffile = os.path.join(referencedir, 'commonGeneFile.txt')
resfile = os.path.join(resultdir, 'commonGeneFile.txt')
self.test_case('example_single.bam', 'example_single.best.sam', '--best --commonGeneFile=' +resfile)
if TestFilterBam.opt_compare:
aug_assertions.assertEqualFiles(
self, reffile, resfile, TestFilterBam.opt_html, htmldir)
os.remove(resfile)
def test_bam2hints_pipes(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, testfilename)
reffile = os.path.join(referencedir, reffilename)
resfile = os.path.join(resultdir, reffilename)
aug_process.execute(self, f'cat {testfile} | {bam2hintsbin}', resfile)
# compare results
if TestBam2Hints.opt_compare:
aug_assertions.assertEqualFiles(self, reffile, resfile,
TestBam2Hints.opt_html, htmldir)
os.remove(resfile)
def test_bam2wig(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, exampletestfile)
reffile = os.path.join(referencedir, 'test.s.wig')
resfile = os.path.join(resultdir, 'test.s.wig')
aug_process.execute(
self, f'{bam2wigbin} {testfile} | grep -v track', resfile)
# compare results
if TestBam2Wig.opt_compare:
aug_assertions.assertEqualFiles(
self, reffile, resfile, TestBam2Wig.opt_html, htmldir)
os.remove(resfile)
def test_bam2wig_region(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, exampletestfile)
reffile = os.path.join(referencedir, 'test.s.chr3L.wig')
resfile = os.path.join(resultdir, 'test.s.chr3L.wig')
aug_process.execute(self,
bam2wigbin + ' -t "my_specified_track" -r chr3L ' + testfile + ' | grep -v track',
resfile)
# compare results
if TestBam2Wig.opt_compare:
aug_assertions.assertEqualFiles(
self, reffile, resfile, TestBam2Wig.opt_html, htmldir)
os.remove(resfile)