def test_full_merge(self):
"""
Tests from main() entry for single star file.
"""
args = FakeArgs()
args.input = [self.star_counts_1, self.star_counts_2]
args.output = self.out_test_pfx + ".1_2.tsv.gz"
self.to_remove.append(args.output)
main(args)
with gzip.open(self.exp_star_1_2,
"rt") as fh, gzip.open(args.output, "rt") as ofh:
exp = fh.read()
found = ofh.read()
self.assertEqual(exp, found)
os.remove(args.output)
def test_full_junction_single(self):
"""
Tests the the whole main() function of junction merge for
a single file.
"""
args = FakeArgs()
args.input = [self.star_junctions_1]
args.output = self.out_test_pfx + ".1.tsv.gz"
self.to_remove.append(args.output)
main(args)
with gzip.open(self.exp_star_1,
"rt") as fh, gzip.open(args.output, "rt") as ofh:
exp = fh.read()
found = ofh.read()
self.assertEqual(exp, found)
os.remove(args.output)
def test_full_run(self):
"""
Full end-to-end test
"""
outfile = 'main_output.tsv'
self.to_remove.append(outfile)
args = FakeArgs()
args.input = self.ts1_counts_file
args.gene_info = self.ts1_gene_info_file
args.output = outfile
args.gencode_version = 36
self.to_remove.append(args.output)
main(args)
result = pd.read_table(args.output, comment='#')
expected = pd.read_table(self.ts1_final_file, comment='#')
pd.testing.assert_frame_equal(result, expected)