def test_output_csv(self):
outfile = self.Blast_dir + "test.csv"
# blast = RunBlast(records=self.record_index, e_value=self.e_threshold, wdir=self.Blast_dir,
# infile=None, outfile=outfile)
data = dict({"GO:01": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 1, })
run_BLAST.output_csv(outfile, "Sample", data)
f = open(outfile, "r")
expected_header = "GOterm,Sample\r\n"
expected_content = ["GO:01,1\r\n",
"GO:03,2\r\n",
"GO:04,2\r\n",
"GO:05,1\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 4)
def test_merge_output_csv_to_MINE(self):
outfile1 = self.working_dir + "test1.csv"
outfile2 = self.working_dir + "test2.csv"
outfile3 = self.working_dir + "test3.csv"
data = dict({"GO:01": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 1, })
run_BLAST.output_csv(outfile1, "Sample", data)
data = dict({"GO:01": 7,
"GO:02": 9,
"GO:04": 2,
"GO:05": 8, })
run_BLAST.output_csv(outfile2, "Species", data)
data = dict({"GO:01": 3,
"GO:02": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 2,
"GO:06": 1,
"GO:07": 1})
run_BLAST.output_csv(outfile3, "Something", data)
outfile = self.working_dir + "test12.csv"
csv_files = [outfile1, outfile2]
run_MINE.merge_output_csv_to_MINE(outfile, csv_files)
f = open(outfile, "r")
expected_header = "Sample_0,Species_1\r\n"
expected_content = ["1,7\r\n",
"2,0\r\n",
"2,2\r\n",
"1,8\r\n",
"0,9\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 5)
outfile = self.working_dir + "test123.csv"
csv_files = [outfile1, outfile2, outfile3]
run_MINE.merge_output_csv_to_MINE(outfile, csv_files, isMINE=False)
f = open(outfile, "r")
expected_header = "GOterm,Sample_0,Species_1,Something_2\r\n"
expected_content = ["GO:01,1,7,3\r\n",
"GO:03,2,0,2\r\n",
"GO:04,2,2,2\r\n",
"GO:05,1,8,2\r\n",
"GO:02,0,9,1\r\n",
"GO:06,0,0,1\r\n",
"GO:07,0,0,1\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 7)
run_MINE.merge_output_csv_to_MINE(outfile, csv_files, isMINE=True)
f = open(outfile, "r")
expected_header = "Sample_0,Species_1,Something_2\r\n"
expected_content = ["1,7,3\r\n",
"2,0,2\r\n",
"2,2,2\r\n",
"1,8,2\r\n",
"0,9,1\r\n",
"0,0,1\r\n",
"0,0,1\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 7)
def test_update_output_csv(self):
outfile1 = self.Blast_dir + "test1.csv"
outfile2 = self.Blast_dir + "test2.csv"
outfile3 = self.Blast_dir + "test3.csv"
# blast = RunBlast(records=self.record_index, e_value=self.e_threshold,
# wdir=self.Blast_dir, outfile=outfile1)
data = dict({"GO:01": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 1, })
run_BLAST.output_csv(outfile1, "Sample", data)
blast = RunBlast(records=self.record_index, e_value=self.e_threshold,
wdir=self.Blast_dir, outfile=outfile2) # , comparison_file="test.csv")
data = dict({"GO:01": 7,
"GO:02": 9,
"GO:04": 2,
"GO:05": 8, })
# blast.output_csv("Species", data)
run_BLAST._update_output_csv(outfile2, "Species", data, existing_csv=outfile1)
f = open(outfile2, "r")
expected_header = "GOterm,Sample,Species\r\n"
expected_content = ["GO:01,1,7\r\n",
"GO:03,2,0\r\n",
"GO:04,2,2\r\n",
"GO:05,1,8\r\n",
"GO:02,0,9\r\n"]
# expected_header = "Sample,Species\r\n"
# expected_content = ["1,7\r\n",
# "2,0\r\n",
# "2,2\r\n",
# "1,8\r\n",
# "0,9\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 5)
new_data = dict({"GO:01": 3,
"GO:02": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 2,
"GO:06": 1,
"GO:07": 1})
# blast.output_csv("Something", new_data)
run_BLAST._update_output_csv(outfile3, "Something", new_data, existing_csv=outfile2)
f = open(outfile3, "r")
expected_header = "GOterm,Sample,Species,Something\r\n"
expected_content = ["GO:01,1,7,3\r\n",
"GO:03,2,0,2\r\n",
"GO:04,2,2,2\r\n",
"GO:05,1,8,2\r\n",
"GO:02,0,9,1\r\n",
"GO:06,0,0,1\r\n",
"GO:07,0,0,1\r\n"]
for i, line in enumerate(f):
if i == 0:
self.assertEqual(line, expected_header)
else:
self.assertIn(line, expected_content)
self.assertEqual(i, 7)
