def test_getNonRedondantDuplications(self):
"""Test getNonRedondantDuplications method"""
iGffDuplicationParser = GffDuplicationParser("test-data/sdd.gff3")
lDuplications = [
Duplication('seq1', 6010863, 6029759, 'seq8', 4391356, 4410272,
[(Region('seq1', 6010863, 6029759,
1), Region('seq8', 4391356, 4410272, 1))]),
Duplication('seq2', 26727, 32020, 'seq11', 521201, 524615,
[(Region('seq2', 26727, 29266,
-1), Region('seq11', 522092, 524615, 1)),
(Region('seq2', 31119, 32020,
-1), Region('seq11', 521201, 522101, 1))]),
Duplication('seq11', 26582, 33594, 'seq11', 584193, 591205,
[(Region('seq11', 26582, 33594,
-1), Region('seq11', 584193, 591205, 1))]),
Duplication('seq11', 38277, 40563, 'seq11', 554466, 556516,
[(Region('seq11', 38277, 38402,
1), Region('seq11', 554466, 554591, 1)),
(Region('seq11', 38511, 40563,
-1), Region('seq11', 554467, 556516, 1))])
]
self.assertEqual(iGffDuplicationParser.getNonRedondantDuplications(),
lDuplications)
def test_getCDSAlignment(self):
"""test getCDSAlignment"""
gene1 = Gene('G00001', 'Chr1', 1, 27, 1, [
Transcript('G00001.1', 'Chr1', 1, 27, 1, 'G00001', [
CDS('G00001.1_cds_1', 'Chr1', 1, 6, 1, 'G00001.1'),
CDS('G00001.1_cds_1', 'Chr1', 13, 21, 1, 'G00001.1')
])
])
gene2 = Gene('G00002', 'Chr5', 1, 27, 1, [
Transcript('G00002.1', 'Chr5', 1, 27, 1, 'G00002', [
CDS('G00002.1_cds_1', 'Chr5', 1, 6, 1, 'G00002.1'),
CDS('G00002.1_cds_1', 'Chr5', 13, 27, 1, 'G00002.1')
])
])
gl = GeneLink(
Duplication('Chr1', 1, 58, 'Chr5', 1, 60, [
(Region('Chr1', 1, 58, 1), Region('Chr5', 1, 60, 1))
], [(
'ATGTATTCTATCTCATGTTAATGCTAATACTAGTCATGATCAGATACGATGATGAT--TA',
'ATGTATTCTATCTCATGTTACTGCTAATACTAGTCATGATCAGATACGATGATGATCATA')
]), gene1, gene2)
self.assertEquals(
('ATGTATtctatcTCATGTTAAtgctaa', 'ATGTATtctatcTCATGTTACTGCTAA',
Region('Chr1', 1, 27, 1), Region('Chr5', 1, 27, 1)),
gl.getCDSAlignment())
gene1 = Gene('G00001', 'Chr1', 1, 27, 1, [
Transcript('G00001.1', 'Chr1', 1, 27, 1, 'G00001', [
CDS('G00001.1_cds_1', 'Chr1', 1, 6, 1, 'G00001.1'),
CDS('G00001.1_cds_1', 'Chr1', 13, 21, 1, 'G00001.1')
])
])
gene2 = Gene('G00002', 'Chr5', 27, 60, -1, [
Transcript('G00002.1', 'Chr5', 27, 60, -1, 'G00002', [
CDS('G00002.1_cds_1', 'Chr5', 27, 39, -1, 'G00002.1'),
CDS('G00002.1_cds_1', 'Chr5', 48, 60, -1, 'G00002.1')
])
])
gl = GeneLink(
Duplication('Chr1', 1, 58, 'Chr5', 1, 60, [
(Region('Chr1', 1, 58, -1), Region('Chr5', 1, 60, 1))
], [(
'ATGTATTCTATCTCATGTTAATGCTAATACTAGTCATGATCAGATACGATGATGAG--TA',
'ATGTATTCTATCTCATGTTACTGCTAATACTAGTCATGATCAGATACGATGATGATCATA')
]), gene1, gene2)
self.assertEquals(
('atactagtcatGATCAGATAcgatgaTGAG--TA',
'ATACTAGTCATGAtcagatacGATGATGATCATA', Region(
'Chr1', 1, 32, -1), Region('Chr5', 27, 60, 1)),
gl.getCDSAlignment())
def test_getSeqAlignment(self):
"""test"""
dup = Duplication('seq1',1,164,'seq2',237,400,[(Region('seq1',1,164,1),Region('seq2',237,400,1))],[('TCCTAGCCGATCTAATCGGAGACTATCTAGGCGACATATAAAATTTTGACGAGCTATAATTATCCTCTAGGCTAATCGAGACCACCGCTATCCTACAGCCAAAACAGCGACTTCATCATCGAGCCGCACTATCCTCTACGGCGAGCGCTCTCTACGAGCATCAT','TCCTAGCCGATCTAATCGGAGACTATCTAGGCGACATATAAAATTTTGACGAGCTATAATTATCCTCTAGGCTAATCGAGACCACCGCTATCCTACAGCCAAAACAGCGACTTCATCATCGAGCCGCACTATCCTCTACGGCGAGCGCTCTCTACGAGCATCAT')])
self.assertEquals('TCCT',dup.getSeqAlignment('seq1',1,4)[0])
dup = Duplication('seq1',1,164,'seq2',237,400,[(Region('seq1',1,164,-1),Region('seq2',237,400,1))],[('TCCTAGCCGATCTAATCGGAGACTATCTAGGCGACATATAAAATTTTGACGAGCTATAATTATCCTCTAGGCTAATCGAGACCACCGCTATCCTACAGCCAAAACAGCGACTTCATCATCGAGCCGCACTATCCTCTACGGCGAGCGCTCTCTACGAGCATCAT','TCCTAGCCGATCTAATCGGAGACTATCTAGGCGACATATAAAATTTTGACGAGCTATAATTATCCTCTAGGCTAATCGAGACCACCGCTATCCTACAGCCAAAACAGCGACTTCATCATCGAGCCGCACTATCCTCTACGGCGAGCGCTCTCTACGAGCATCAT')])
self.assertEquals('TCAT',dup.getSeqAlignment('seq1',1,4)[0])
dup = Duplication('seq4',1,40,'seq5',20,30,[(Region('seq4',1,10,-1),Region('seq5',20,25,1)),(Region('seq4',35,40,-1),Region('seq5',25,30,1))],[('ATATATATAT','AT----ATAT'),('ATGT-TT','AT-TTTG')])
self.assertEquals('ATGT',dup.getSeqAlignment('seq4',37,40)[0])
self.assertEquals('T----ATAT',dup.getSeqAlignment('seq5',21,25)[0])
def test_writeSegDupDataFile(self):
"""Test writeSegDupDataFile"""
lDuplications = [Duplication('seq1',5,5000,'seq2',10,5000)]
SDDataFile = self.plot.writeSegDupDataFile(lDuplications,'segdup.txt')
self.assertTrue(filecmp.cmp(SDDataFile,'test-data/segdup.txt'))
os.remove('segdup.txt')
def test_writeCircosConf(self):
"""Test writeCircosConf"""
lSeqs = [('seq1',20000),('seq2',30000)]
GenomeDataFile = self.plot.writeSeqDataFile(lSeqs, 'genome.txt')
lRegions = [(Region('seq1',100,220,1),Region('seq2',100,220,1)),
(Region('seq1',1200,1300,-1),Region('seq2',1300,1400,1))]
lAlgmts = [('ATGCATGCATGCATGCATGCATGCATGCATGCATGCAGGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATATGTGTAGTGAGTCGTCCC',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGATGTACGATATAGCCCAC'),
('ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA')]
lDuplications = [Duplication('seq1',1,5000,'seq2',1,6000,lRegions,lAlgmts)]
SDDataFile = self.plot.writeSegDupDataFile(lDuplications,'segdup.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos.conf'))
lGenes = [Gene('GENE1','seq1',12,600,1),Gene('GENE2','seq2',100,1000,-1)]
GeneDataFile = self.plot.writeGeneDataFile(lGenes,'gene.txt')
lTEs = [Feature('TE1','seq1',1000,2000,1,'TE'),Feature('TE2','seq2',4000,4500,-1,'TE')]
TEDataFile = self.plot.writeTEDataFile(lTEs,'TE.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos2.conf'))
SimilarityDataFile = self.plot.writeSimilarityDataFile(lDuplications,'similarity.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos3.conf'))
os.remove('circos.conf')
def test_writeGeneLinkDataFile(self):
"""Test writeGeneLinkDataFile"""
iDup = Duplication('seq1',5,5000,'seq2',10,5000)
iGene1 = Gene('GENE1','seq1',10,100,1)
iGene2 = Gene('GENE2','seq2',100,190,-1)
lGeneLinks = [GeneLink(dup=iDup,gene1=iGene1,gene2=iGene2)]
GeneLinkDataFile = self.plot.writeGeneLinkDataFile(lGeneLinks,'gene-link.txt')
self.assertTrue(filecmp.cmp(GeneLinkDataFile,'test-data/gene-link.txt'))
os.remove('gene-link.txt')
def test_writeSimilarityDataFile(self):
"""Test writeSimilarityDataFile"""
lRegions = [(Region('seq1',100,220,1),Region('seq2',100,220,1)),
(Region('seq1',1200,1300,-1),Region('seq2',1300,1400,1))]
lAlgmts = [('ATGCATGCATGCATGCATGCATGCATGCATGCATGCAGGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATATGTGTAGTGAGTCGTCCC',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGATGTACGATATAGCCCAC'),
('ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA')]
lDuplications = [Duplication('seq1',1,5000,'seq2',1,6000,lRegions,lAlgmts)]
SimilarityDataFile = self.plot.writeSimilarityDataFile(lDuplications,'similarity.txt')
self.assertTrue(filecmp.cmp(SimilarityDataFile,'test-data/similarity.txt'))
os.remove('similarity.txt')
def _buildDuplication(self,seq1Dup,lRegions):
"""build duplication"""
# define seq2 boundaries
seq2 = None
seq2Start = 999999999999
seq2End = 0
for reg1,reg2 in lRegions:
if reg2.start < seq2Start:
seq2Start = reg2.start
if reg2.end > seq2End:
seq2End = reg2.end
seq2 = reg2.seq
seq2Dup = (seq2,int(seq2Start),int(seq2End))
# create and return Duplication
return Duplication(seq1Dup[0],seq1Dup[1],seq1Dup[2],seq2Dup[0],seq2Dup[1],seq2Dup[2],lRegions)
def test_dSeqToSeq(self):
"""Duplication with alignment"""
dSeqToSeq = {'seq1': {1: ('seq1', 1), 2: ('seq1', 2),
3: ('seq1', 3), 4: ('seq1', 4),
5: ('seq1', 5)}}
dup = Duplication('seq1', 1, 5, 'seq1', 1, 5, [(Region('seq1', 1, 5, 1),
Region('seq1', 1, 5, 1))], [('ATGAT', 'ATGAT')])
self.maxDiff = None
self.assertEqual(dSeqToSeq,dup.dSeqToSeq)
dSeqToSeq = {'seq2': {54: ('seq2', 302), 55: ('seq2', 301),
56: ('seq2', 300), 57: ('seq2', None),
58: ('seq2', 299), 59: ('seq2', 298),
60: ('seq2', 297), 61: ('seq2', 295),
62: ('seq2', 294), 63: ('seq2', 293),
64: ('seq2', None), 65: ('seq2', 292),
66: ('seq2', 291), 67: ('seq2', 290),
68: ('seq2', 289), 69: ('seq2', 288),
288: ('seq2', 69), 289: ('seq2', 68),
290: ('seq2', 67), 291: ('seq2', 66),
292: ('seq2', 65), 293: ('seq2', 63),
294: ('seq2', 62), 295: ('seq2', 61),
296: ('seq2', None), 297: ('seq2', 60),
298: ('seq2', 59), 299: ('seq2', 58),
300: ('seq2', 56), 301: ('seq2', 55),
302: ('seq2', 54)}}
dup = Duplication('seq2', 288, 302, 'seq2', 54, 69, [(Region('seq2',288, 302, -1),
Region('seq2', 54, 69, 1))],[('TGA-AGTCGCT-GTTTT', 'TGATAGT-GCTGGTTTT')])
self.maxDiff = None
self.assertEqual(dSeqToSeq,dup.dSeqToSeq)
dSeqToSeq = {'seq1': {1: ('seq2', 241), 2: ('seq2', 240),
3: ('seq2', 239), 4: ('seq2', 238),
5: ('seq2', 237)},
'seq2': {237: ('seq1', 5), 238: ('seq1', 4),
239: ('seq1', 3), 240: ('seq1', 2),
241: ('seq1', 1)}}
dup = Duplication('seq1', 1, 5, 'seq2', 237, 241, [(Region('seq1', 1, 5, -1),
Region('seq2', 237, 241, 1))],[('TCCTA', 'TCCTA')])
self.maxDiff = None
self.assertEqual(dSeqToSeq,dup.dSeqToSeq)
dSeqToSeq = {'Chr1': {1: ('Chr5', 60), 2: ('Chr5', 59),
3: ('Chr5', 56), 4: ('Chr5', 55),
5: ('Chr5', 54), 6: ('Chr5', 53),
7: ('Chr5', 52), 8: ('Chr5', 51),
9: ('Chr5', 50), 10: ('Chr5', 49),
11: ('Chr5', 48), 12: ('Chr5', 47),
13: ('Chr5', 46), 14: ('Chr5', 45),
15: ('Chr5', 44), 16: ('Chr5', 43),
17: ('Chr5', 42), 18: ('Chr5', 41),
19: ('Chr5', 40), 20: ('Chr5', 39),
21: ('Chr5', 38), 22: ('Chr5', 37),
23: ('Chr5', 36), 24: ('Chr5', 35),
25: ('Chr5', 34), 26: ('Chr5', 33),
27: ('Chr5', 32), 28: ('Chr5', 31),
29: ('Chr5', 30), 30: ('Chr5', 29),
31: ('Chr5', 28), 32: ('Chr5', 27),
33: ('Chr5', 26), 34: ('Chr5', 25),
35: ('Chr5', 24), 36: ('Chr5', 23),
37: ('Chr5', 22), 38: ('Chr5', 21),
39: ('Chr5', 20), 40: ('Chr5', 19),
41: ('Chr5', 18), 42: ('Chr5', 17),
43: ('Chr5', 16), 44: ('Chr5', 15),
45: ('Chr5', 14), 46: ('Chr5', 13),
47: ('Chr5', 12), 48: ('Chr5', 11),
49: ('Chr5', 10), 50: ('Chr5', 9),
51: ('Chr5', 8), 52: ('Chr5', 7),
53: ('Chr5', 6), 54: ('Chr5', 5),
55: ('Chr5', 4), 56: ('Chr5', 3),
57: ('Chr5', 2), 58: ('Chr5', 1)},
'Chr5': {1: ('Chr1', 58), 2: ('Chr1', 57),
3: ('Chr1', 56), 4: ('Chr1', 55),
5: ('Chr1', 54), 6: ('Chr1', 53),
7: ('Chr1', 52), 8: ('Chr1', 51),
9: ('Chr1', 50), 10: ('Chr1', 49),
11: ('Chr1', 48), 12: ('Chr1', 47),
13: ('Chr1', 46), 14: ('Chr1', 45),
15: ('Chr1', 44), 16: ('Chr1', 43),
17: ('Chr1', 42), 18: ('Chr1', 41),
19: ('Chr1', 40), 20: ('Chr1', 39),
21: ('Chr1', 38), 22: ('Chr1', 37),
23: ('Chr1', 36), 24: ('Chr1', 35),
25: ('Chr1', 34), 26: ('Chr1', 33),
27: ('Chr1', 32), 28: ('Chr1', 31),
29: ('Chr1', 30), 30: ('Chr1', 29),
31: ('Chr1', 28), 32: ('Chr1', 27),
33: ('Chr1', 26), 34: ('Chr1', 25),
35: ('Chr1', 24), 36: ('Chr1', 23),
37: ('Chr1', 22), 38: ('Chr1', 21),
39: ('Chr1', 20), 40: ('Chr1', 19),
41: ('Chr1', 18), 42: ('Chr1', 17),
43: ('Chr1', 16), 44: ('Chr1', 15),
45: ('Chr1', 14), 46: ('Chr1', 13),
47: ('Chr1', 12), 48: ('Chr1', 11),
49: ('Chr1', 10), 50: ('Chr1', 9),
51: ('Chr1', 8), 52: ('Chr1', 7),
53: ('Chr1', 6), 54: ('Chr1', 5),
55: ('Chr1', 4), 56: ('Chr1', 3),
57: ('Chr1', None), 58: ('Chr1', None),
59: ('Chr1', 2), 60: ('Chr1', 1)}}
dup = Duplication('Chr1' ,1 ,58 ,'Chr5' ,1 ,60 ,
[(Region('Chr1' ,1 ,58 ,-1),Region('Chr5',1,60,1))],
[('ATGTATTCTATCTCATGTTAATGCTAATACTAGTCATGATCAGATACG'
'ATGATGAG--TA',
'ATGTATTCTATCTCATGTTACTGCTAATACTAGTCATGATCAGATACG'
'ATGATGATCATA')])
self.maxDiff = None
self.assertEqual(dSeqToSeq,dup.dSeqToSeq)