Python _softclip_to_first_match Examples

Example #1

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

 def test_softclip_to_first_match_uncommonMatchOpOk(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS" "XPNDISH"),
                       util._softclip_to_first_match(42, "SDNIP" "XPNDISH"))
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS" "=PNDISH"),
                       util._softclip_to_first_match(42, "SDNIP" "=PNDISH"))

Example #2

 def test_softclip_to_first_match_uncommonMatchOpOk(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS"
                        "XPNDISH"),
                       util._softclip_to_first_match(42, "SDNIP"
                                                     "XPNDISH"))
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS"
                        "=PNDISH"),
                       util._softclip_to_first_match(42, "SDNIP"
                                                     "=PNDISH"))

Example #3

 def test_softclip_to_first_match_posIsAdjusted(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS"
                        "MPNDISH"),
                       util._softclip_to_first_match(42, "SDNIP"
                                                     "MPNDISH"))

Example #4

 def test_softclip_to_first_noMatchesPassesThrough(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS"), util._softclip_to_first_match(45, "SS"))

Example #5

 def test_softclip_to_first_match(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "MM"), util._softclip_to_first_match(45, "MM"))

Example #6

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

 def test_softclip_to_first_match_posIsAdjusted(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS" "MPNDISH"),
                       util._softclip_to_first_match(42, "SDNIP" "MPNDISH"))

Example #7

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

 def test_softclip_to_first_noMatchesPassesThrough(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "SS"),
                       util._softclip_to_first_match(45, "SS"))

Example #8

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

 def test_softclip_to_first_match(self):
     util = cigar.CigarUtil(0, "1M")
     self.assertEquals((45, "MM"),
                       util._softclip_to_first_match(45, "MM"))