def test_filter_raises_error_on_empty_filtered_result(self):
''' This should raise an AssertionError because no reads will be left after that quality filter.'''
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
write_filtered(self.inputfn, 65, True)
self.assertEquals(len(w), 1)
def test_filter_raises_error_on_empty_filtered_result(self):
''' This should raise an AssertionError because no reads will be left after that quality filter.'''
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
write_filtered(self.inputfn, 65, True)
self.assertEquals(len(w), 1)
def test_symlink_file_none_filtered(self):
write_filtered(self.inputfn, 0, False, outdir=self.outdir)
self.assertTrue(os.path.islink(self.actualfn))
def test_write_filtered_unfiltered(self):
''' input and output fastq files should be the same if filters make everything pass '''
write_filtered(self.inputfn, 0, False, outdir=self.outdir)
self.assertFilesEqual(self.inputfn, self.actualfn)
def test_symlink_file_none_filtered(self):
write_filtered(self.inputfn, 0, False, outdir=self.outdir)
self.assertTrue(os.path.islink(self.actualfn))
def test_write_filtered_unfiltered(self):
''' input and output fastq files should be the same if filters make everything pass '''
write_filtered(self.inputfn, 0, False, outdir=self.outdir)
self.assertFilesEqual(self.inputfn, self.actualfn)