class TestClass:
def __init__(self):
self.importer = Importer(":memory:")
def setUp(self):
print "SETUP!"
self.ccdsLine = [
"1",
"NC_000001.10",
"SAMD11",
"148398",
"CCDS2.2",
"Public",
"+",
"861321",
"879532",
"[861321-861392, 865534-865715, 866418-866468, 871151-"
"871275, 874419-874508, 874654-874839, 876523-876685, "
"877515-877630, 877789-877867, 877938-878437, 878632-"
"878756, 879077-879187, 879287-879532]",
"Identical",
]
self.exonString = "[861321-861392, 865534-865715, 866418-866468]"
def tearDown(self):
print "TEAR DOWN!"
def test_extractLineData(self):
(chrom, hgnc, txId, strand, txStart, txEnd, exons) = self.importer._extractLineData(self.ccdsLine)
assert_equal(chrom, "1")
assert_equal(hgnc, "SAMD11")
assert_equal(txId, "CCDS2.2")
assert_equal(txStart, 861320)
assert_equal(txEnd, 879531)
assert_equal(strand, "+")
def test_generateExonCoordinates(self):
exons = self.importer._generateExonCoordinates(self.exonString)
assert_equal(exons, [[861320, 861391], [865533, 865714], [866417, 866467]])
def __init__(self):
self.importer = Importer(":memory:")