def testMismatchNames(self):
trans = {"start": 1, "stop": 648, "name": "not a name"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for name mismatch.")
except:
pass
def testMismatchNames(self):
trans = {"start":1, "stop": 648, "name":"not a name"}
try:
cds = build_coordinates(self.gene,trans)
self.fail("expected exception for name mismatch.")
except:
pass
def testMiddle(self):
trans = {"start": 147, "stop": 550, "name":"off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{ "start": 301, "stop": 700},
{ "start": 801, "stop": 804}
]
self.assertEqual(expect, cds, "included last region")
def testNegativeNumbers(self):
trans = {"start": -200, "stop": 400, "name": "off1end"}
try:
cds = build_coordinates(self.gene,trans)
self.fail("expected exception for negative number.")
except:
pass
trans = {"start": 200, "stop": -400, "name": "off1end"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for negative number")
except:
pass
trans = {"start": -200, "stop": -100, "name": "off1end"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for negative number")
except:
pass
def testTooShort(self):
trans = {"start": 1, "stop": 646, "name":"off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{ "start": 101, "stop": 105},
{ "start": 111, "stop": 200},
{ "start": 225, "stop": 275},
{ "start": 301, "stop": 700},
{ "start": 801, "stop": 900}
]
self.assertEqual(expect, cds, "included last region") #should map off by one
def testNegativeNumbers(self):
trans = {"start": -200, "stop": 400, "name": "off1end"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for negative number.")
except:
pass
trans = {"start": 200, "stop": -400, "name": "off1end"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for negative number")
except:
pass
trans = {"start": -200, "stop": -100, "name": "off1end"}
try:
cds = build_coordinates(self.gene, trans)
self.fail("expected exception for negative number")
except:
pass
def testCorrectPlusPlus(self):
"""
Plus Plus works exactly as expected. No reverse transcription required. ATG appears immediately
at final[522:3012], and the sequence in the transdecoder.cds match the subsequence.
"""
gene = {'start': 74641, 'stop': 78761, 'name':'plusplus',
'exons': ({ 'start': 74641, 'stop': 76014 } ,
{ 'start': 76111, 'stop': 76277 } ,
{ 'start': 76368, 'stop': 76465 } ,
{ 'start': 76558, 'stop': 76914 } ,
{ 'start': 77029, 'stop': 77445 } ,
{ 'start': 77628, 'stop': 78761 }
)}
transcript = {'name':'plusplus', 'start': 523, 'stop':3012}
cds = build_coordinates(gene, transcript) #??? what should this do...
# should equal start-1:stop
self.assertEqual(self.plusplusgen[522:3012], self.plusplusorf)
def testTooShort(self):
trans = {"start": 1, "stop": 646, "name": "off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{
"start": 101,
"stop": 105
}, {
"start": 111,
"stop": 200
}, {
"start": 225,
"stop": 275
}, {
"start": 301,
"stop": 700
}, {
"start": 801,
"stop": 900
}]
self.assertEqual(expect, cds,
"included last region") #should map off by one
def testCorrectPlusPlus(self):
"""
Plus Plus works exactly as expected. No reverse transcription required. ATG appears immediately
at final[522:3012], and the sequence in the transdecoder.cds match the subsequence.
"""
gene = {
'start':
74641,
'stop':
78761,
'name':
'plusplus',
'exons': ({
'start': 74641,
'stop': 76014
}, {
'start': 76111,
'stop': 76277
}, {
'start': 76368,
'stop': 76465
}, {
'start': 76558,
'stop': 76914
}, {
'start': 77029,
'stop': 77445
}, {
'start': 77628,
'stop': 78761
})
}
transcript = {'name': 'plusplus', 'start': 523, 'stop': 3012}
cds = build_coordinates(gene, transcript) #??? what should this do...
# should equal start-1:stop
self.assertEqual(self.plusplusgen[522:3012], self.plusplusorf)
def testSingleExon(self):
trans = {"start":6, "stop": 48, "name":"off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{"start": 111, "stop":153}]
self.assertEqual(expect, cds)
def testTooLong(self):
trans = {"start": 1, "stop": 648, "name":"off1end"}
cds = build_coordinates(self.gene, trans)
self.assertEqual(self.gene['exons'], cds, "Did not correct for an input that goes past maximum length")
def testPerfectMatch(self):
trans = {"start": 1, "stop": 647, "name":"off1end"}
cds = build_coordinates(self.gene, trans)
self.assertEqual(self.gene['exons'], cds, "Full gene does not match.") #should map perfectly
def testSingleExon(self):
trans = {"start": 6, "stop": 48, "name": "off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{"start": 111, "stop": 153}]
self.assertEqual(expect, cds)
def testMiddle(self):
trans = {"start": 147, "stop": 550, "name": "off1end"}
cds = build_coordinates(self.gene, trans)
expect = [{"start": 301, "stop": 700}, {"start": 801, "stop": 804}]
self.assertEqual(expect, cds, "included last region")
def testTooLong(self):
trans = {"start": 1, "stop": 648, "name": "off1end"}
cds = build_coordinates(self.gene, trans)
self.assertEqual(
self.gene['exons'], cds,
"Did not correct for an input that goes past maximum length")
def testPerfectMatch(self):
trans = {"start": 1, "stop": 647, "name": "off1end"}
cds = build_coordinates(self.gene, trans)
self.assertEqual(self.gene['exons'], cds,
"Full gene does not match.") #should map perfectly