def testAddColumn(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"), uniqKeyCols="qName")
tsv.addColumn("joke")
i = 0
for row in tsv:
row.joke = i
i += 1
fh = open(self.getOutputFile(".tsv"), "w")
tsv.write(fh)
fh.close()
self.diffExpected(".tsv")
def testColTypeDefault(self):
# default to int type
typeMap = {
"strand": str,
"qName": str,
"tName": str,
"blockSizes": intArrayType,
"qStarts": intArrayType,
"tStarts": intArrayType
}
tsv = TSVTable(self.getInputFile("mrna1.tsv"),
uniqKeyCols="qName",
typeMap=typeMap,
defaultColType=int)
r = tsv.idx.qName["AK095183"]
self.failUnlessEqual(r.tStart, 4222)
self.failUnlessEqual(r.tEnd, 19206)
self.failUnlessEqual(r.tName, "chr1")
self.failUnlessEqual(r.tStart, 4222)
tStarts = (4222, 4832, 5658, 5766, 6469, 6719, 7095, 7355, 7777, 8130,
14600, 19183)
self.failUnlessEqual(len(r.tStarts), len(tStarts))
for i in xrange(len(tStarts)):
self.failUnlessEqual(r.tStarts[i], tStarts[i])
def testMissingIdxCol(self):
err = None
try:
tsv = TSVTable(self.getInputFile("mrna1.tsv"),
multiKeyCols=("noCol", ))
except TSVError, e:
err = e
def testLoad(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"))
self.failUnlessEqual(len(tsv), 10)
for r in tsv:
self.failUnlessEqual(len(r), 22)
r = tsv[0]
self.failUnlessEqual(r["qName"], "BC032353")
self.failUnlessEqual(r[10], "BC032353")
self.failUnlessEqual(r.qName, "BC032353")
def testMultiIdx(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"),
multiKeyCols=("tName", "tStart"))
rows = tsv.idx.tName["chr1"]
self.failUnlessEqual(len(rows), 10)
self.failUnlessEqual(rows[1].qName, "AK095183")
rows = tsv.idx.tStart["4268"]
self.failUnlessEqual(len(rows), 5)
self.failUnlessEqual(rows[0].qName, "BC015400")
def testAddColumn(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"), uniqKeyCols="qName")
tsv.addColumn("joke")
i = 0
for row in tsv:
row.joke = i
i += 1
fh = open(self.getOutputFile(".tsv"), "w")
tsv.write(fh)
fh.close()
self.diffExpected(".tsv")
def doTestColType(self, inFile):
typeMap = {
"intCol": int,
"floatCol": float,
"onOffCol": (self.onOffParse, self.onOffFmt)
}
tsv = TSVTable(self.getInputFile(inFile), typeMap=typeMap)
r = tsv[0]
self.failUnlessEqual(r.strCol, "name1")
self.failUnlessEqual(r.intCol, 10)
self.failUnlessEqual(r.floatCol, 10.01)
self.failUnlessEqual(str(r), "name1\t10\t10.01\ton")
r = tsv[2]
self.failUnlessEqual(r.strCol, "name3")
self.failUnlessEqual(r.intCol, 30)
self.failUnlessEqual(r.floatCol, 30.555)
self.failUnlessEqual(str(r), "name3\t30\t30.555\toff")
def testColNameMap(self):
typeMap = {
"int_col": int,
"float_col": float,
"onOff_col": (self.onOffParse, self.onOffFmt)
}
tsv = TSVTable(self.getInputFile('typesColNameMap.tsv'),
typeMap=typeMap,
columnNameMapper=lambda s: s.replace(' ', '_'))
r = tsv[0]
self.failUnlessEqual(r.str_col, "name1")
self.failUnlessEqual(r.int_col, 10)
self.failUnlessEqual(r.float_col, 10.01)
self.failUnlessEqual(str(r), "name1\t10\t10.01\ton")
r = tsv[2]
self.failUnlessEqual(r.str_col, "name3")
self.failUnlessEqual(r.int_col, 30)
self.failUnlessEqual(r.float_col, 30.555)
self.failUnlessEqual(str(r), "name3\t30\t30.555\toff")
def testAllowEmptyTbl(self):
tbl = TSVTable("/dev/null", allowEmpty=True)
self.failUnlessEqual(len(tbl), 0)
def testDupColumn(self):
err = None
try:
tsv = TSVTable(self.getInputFile("dupCol.tsv"))
except TSVError, e:
err = e
def testWrite(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"), uniqKeyCols="qName")
fh = open(self.getOutputFile(".tsv"), "w")
tsv.write(fh)
fh.close()
self.diffExpected(".tsv")
def testWrite(self):
tsv = TSVTable(self.getInputFile("mrna1.tsv"), uniqKeyCols="qName")
fh = open(self.getOutputFile(".tsv"), "w")
tsv.write(fh)
fh.close()
self.diffExpected(".tsv")