def test_subset_Feature_working(self):
res = BedFileParser.search_featurename(self.df, name="genex")
expected = pd.DataFrame(columns=["chrom", "start", "end", "name", "strand"],
data=[["1", 3, 2442, "genex", "-"]])
if res.equals(expected):
self.assertTrue("Feature subset working")
else:
self.assertFalse("Feature subset working")
def test_subset_Pos_working(self):
res = BedFileParser.search_position(self.df, chrom="chr1", start=1, end=2500)
expected = pd.DataFrame(columns=["chrom", "start", "end", "name", "strand"],
data=[["1", 3, 2442, "genex", "-"]])
if res.equals(expected):
self.assertTrue("Positional subset working")
else:
self.assertFalse("Positional subset working")
def test_subset_Chr_working(self):
res = BedFileParser.search_position(self.df, chrom="chr1")
expected = pd.DataFrame(columns=["chrom", "start", "end", "name", "strand"],
data=[["1", 1, 2999, "gene1", "+"],
["1", 3, 2442, "genex", "-"]])
if res.equals(expected):
self.assertTrue("Chromosome subset working")
else:
self.assertFalse("Chromosome subset not working")
def test_fileload_working(self):
df_actual = BedFileParser.load_file("data/test_bed_working.bed")
df_expected = pd.DataFrame(columns=["chrom", "start", "end", "name", "strand"],
data=[["1", 1, 2999, "gene1", "+"],
["1", 3, 2442, "genex", "-"],
["2", 8000, 74000, "gene2", "+"],
["3", 3000, 9000, "gene3", "-"]])
if df_actual.equals(df_expected):
self.assertTrue("File loaded properly")
else:
self.assertFalse("File cannot be loaded")
def test_summary_working(self):
res = BedFileParser.summary_statistics(self.df).to_csv()
expected = pd.DataFrame(
columns=["chrom", "TotalFeatures", "NumFeaturesPos", "NumFeaturesNeg", "min", "max", "mean"],
data=[[1, 2, 1.0, 1.0, 2439, 2998, 2718.5],
[2, 1, 1.0, 0.0, 66000, 66000, 66000.0],
[3, 1, 0.0, 1.0, 6000, 6000, 6000.0]]
)
expected.set_index('chrom', inplace=True)
expected_csv = expected.to_csv()
if res == expected_csv:
self.assertTrue("Summary is working")
else:
self.assertFalse("Summary is not working")
def test_subset_feature(self):
self.assertRaises(BedFileParser.IncorrectFeatureName, lambda: BedFileParser.search_featurename(self.df,
name="genex!"))
def test_subset_coord(self):
self.assertRaises(BedFileParser.IncorrectCoord, lambda: BedFileParser.search_position(self.df, chrom="chr1",
start=3000, end=1))
def test_subset_chr(self):
self.assertRaises(BedFileParser.IncorrectChr, lambda: BedFileParser.search_position(self.df, chrom="1"))
def setUp(self):
self.df = BedFileParser.load_file('data/test_bed_working.bed')
def test_fileload_strand(self):
self.assertRaises(BedFileParser.IncorrectStrand, lambda: BedFileParser.load_file("data/test_bed_strand.bed"))
def test_fileload_feature(self):
self.assertRaises(BedFileParser.IncorrectFeatureName, lambda: BedFileParser.load_file("data/"
"test_bed_feature.bed"))
def test_fileload_coord(self):
self.assertRaises(BedFileParser.IncorrectCoord, lambda: BedFileParser.load_file("data/test_bed_coord.bed"))
def test_fileload_chr(self):
self.assertRaises(BedFileParser.IncorrectChr, lambda: BedFileParser.load_file("data/test_bed_chr.bed"))