def testUnalignedReference(self):
expectedFwdNative = "GCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC"
EQ(expectedFwdNative, self.fwdAln.reference(aligned=False))
EQ(expectedFwdNative, self.fwdAln.reference(aligned=False, orientation="genomic"))
expectedRevNative = "TAGCCACCGGATATCCCACAGGTGAGCCGTGTAGTTGAAGGTTTTTACGTCAGATTCTTTTGGGATTGGCTTGGGTTTATTTCTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATGTCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
EQ(expectedRevNative, self.revAln.reference(aligned=False))
EQ(RC(expectedRevNative), self.revAln.reference(aligned=False, orientation="genomic"))
def testAlignedReference(self):
expectedFwdNative = 'GCCGCGCTGGATG--AACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTG-AATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTAC-TTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC'
EQ(expectedFwdNative, self.fwdAln.reference(aligned=True))
EQ(expectedFwdNative, self.fwdAln.reference())
EQ(expectedFwdNative, self.fwdAln.reference(orientation="genomic"))
expectedRevNative = 'TAGCCACCGGATATC-CCACAGGTGA-GCCGTGT-AGTTGAAGG-TTTT-TACGTCAGATTCTTTTGGGATT-GGCTTGGGTTTATTT-CTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATG--T-CGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC'
EQ(expectedRevNative, self.revAln.reference(aligned=True))
EQ(expectedRevNative, self.revAln.reference())
EQ(RC(expectedRevNative), self.revAln.reference(orientation="genomic"))
def testAlignedRead(self):
expectedFwdNative = "GCCGCGAT-GATGAAAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTT-ACAGGCTGCGGCATTTTGTCCGCGCC-GGCTTCGCTCACTGTTCAGGCCGGAG-CACAGACCGCCGTTGAAATGGGCGGATGCTAATTACTATCTCCCGAAAGAAT-CGC-TACCAGGAAGGGCGATGGGAAACACTGCCCTTTCAGCGGG-CATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGT-AATGTGGTGAAGTCTG-CCGTGTCGGTTATTCCAAAATGCTGCTGGGTG-TTATGCCT-CGTTTATAGAGCATAAGCAGCGCAACA-CCTTATCTGGTTGCC"
EQ(expectedFwdNative, self.fwdAln.read(aligned=True))
EQ(expectedFwdNative, self.fwdAln.read())
EQ(expectedFwdNative, self.fwdAln.read(orientation="genomic"))
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTG-AGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTT-GAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
EQ(expectedRevNative, self.revAln.read(aligned=True))
EQ(expectedRevNative, self.revAln.read())
EQ(RC(expectedRevNative), self.revAln.read(orientation="genomic"))
def testUnalignedRead(self):
expectedFwdNative = 'GCCGCGATGATGAAAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTACAGGCTGCGGCATTTTGTCCGCGCCGGCTTCGCTCACTGTTCAGGCCGGAGCACAGACCGCCGTTGAAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCGCTACCAGGAAGGGCGATGGGAAACACTGCCCTTTCAGCGGGCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTAATGTGGTGAAGTCTGCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTATGCCTCGTTTATAGAGCATAAGCAGCGCAACACCTTATCTGGTTGCC'
assert expectedFwdNative == self.fwdAln.read(aligned=False)
assert expectedFwdNative == self.fwdAln.read(aligned=False,
orientation="genomic")
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTGAGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTTGAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
assert expectedRevNative == self.revAln.read(aligned=False)
assert RC(expectedRevNative) == self.revAln.read(aligned=False,
orientation="genomic")
def testAlignedReference(self):
expectedFwdNative = "TACGGTCATCATCTGACACTACAGACTCTGGCATCGCTGTGAAGAC"
EQ(expectedFwdNative, self.fwdAln.reference(aligned=True))
EQ(expectedFwdNative, self.fwdAln.reference())
EQ(expectedFwdNative, self.fwdAln.reference(orientation="genomic"))
expectedRevNative = "CTTGTGAAAATGCTGAATT-TCGCGTCGTCTTCA-CAGCGATGCCAGAGTCTGTAGTGTCA"
EQ(expectedRevNative, self.revAln.reference(aligned=True))
EQ(expectedRevNative, self.revAln.reference())
EQ(RC(expectedRevNative), self.revAln.reference(orientation="genomic"))
def testUnalignedRead(self):
expectedFwdNative = "TACGGTCATCATCTGACACTACAGACTCTGGCATCGCTGTGAAGAC"
EQ(expectedFwdNative, self.fwdAln.read(aligned=False))
EQ(expectedFwdNative,
self.fwdAln.read(aligned=False, orientation="genomic"))
expectedRevNative = "CTTGTGAAAATGCTGAATTCTGCGTCGCTTCACCAGCGATGCCAAGTCTGTAGTGTCA"
EQ(expectedRevNative, self.revAln.read(aligned=False))
EQ(RC(expectedRevNative),
self.revAln.read(aligned=False, orientation="genomic"))