Python _pos_profiles Examples

Example #1

 def test_pos_profiles_trailingHardclips(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SDMHH")
     self.assertEquals((2, ["S", "D", "M", "HH"]), actual)

Example #2

 def test_pos_profiles_insertOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SIM")
     self.assertEquals((1, ["S", "IM"]), actual)

Example #3

 def test_pos_profiles_deleteOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SDM")
     self.assertEquals((2, ["S", "D", "M"]), actual)

Example #4

 def test_pos_profiles_uncommonMatchOpOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("=MM")
     self.assertEquals((0, ["=", "M", "M"]), actual)

Example #5

 def test_pos_profiles_leadingSoftclips(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SMM")
     self.assertEquals((1, ["S", "M", "M"]), actual)

Example #6

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles_trailingHardclips(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SDMHH")
     self.assertEquals((2, ["S", "D", "M", "HH"]), actual)

Example #7

 def test_pos_profiles(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("MMM")
     self.assertEquals((0, ["M", "M", "M"]), actual)

Example #8

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles_deleteOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SDM")
     self.assertEquals((2, ["S", "D", "M"]), actual)

Example #9

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles_insertOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SIM")
     self.assertEquals((1, ["S", "IM"]), actual)

Example #10

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles_leadingSoftclips(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("SMM")
     self.assertEquals((1, ["S", "M", "M"]), actual)

Example #11

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles_uncommonMatchOpOk(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("=MM")
     self.assertEquals((0, ["=", "M", "M"]), actual)

Example #12

File: cigar_test.py Project: umich-brcf-bioinf/Katana

 def test_pos_profiles(self):
     util = cigar.CigarUtil(0, "1M")
     actual = util._pos_profiles("MMM")
     self.assertEquals((0, ["M", "M", "M"]), actual)