def test_validate_num_rows(self):
file = self.exampleFile(filename)
dataframe = read_bed(file)
with open(file, "r") as ins:
lines = []
for line in ins:
lines.append(line)
assert (len(lines) == len(dataframe.index))
def test_to_json(self):
dataframe = read_bed(self.exampleFile(filename))
def is_valid_json(string):
try:
json_object = json.loads(string)
except ValueError:
return False
return True
assert (type(dataframe._mango_to_json) == str)
assert (is_valid_json(dataframe._mango_to_json) == True)
def test_column_type(self):
dataframe = read_bed(self.exampleFile("chr17.582500-594500.bed"))
chromosomes = list(dataframe["chrom"])
chromStart = list(dataframe["chromStart"])
chromEnd = list(dataframe["chromEnd"])
for i in range(len(chromStart)):
assert (type(chromStart[i] == int))
for i in range(len(chromEnd)):
assert (type(chromEnd[i] == int))
for i in range(len(chromosomes)):
assert (type(chromosomes[i] == int))
def test_visualization(self):
dataframe = read_bed(self.exampleFile(filename))
assert (dataframe._pileup_visualization == "featureJson")
tracks = [
Track(viz="features",
label="my features",
source=pileup.sources.DataFrameSource(dataframe))
]
reads = pileup.PileupViewer(chrom="chr22",
start=10436,
stop=10564,
reference="hg19",
tracks=tracks)
assert (str(
type(reads)
) == '<class \'bdgenomics.mango.pileup.pileupViewer.PileupViewer\'>')
assert (reads.chrom == 'chr22')
def test_required_columns(self):
dataframe = read_bed(self.exampleFile(filename))
dataframe_columns = list(dataframe.columns)
for name in ("chrom", "chromStart", "chromEnd"):
assert (name in dataframe_columns)