def setUp(self):
b1_hg19_seq = "<STR_LIT>"<EOL>b1_panTro_s = "<STR_LIT>"<EOL>b1_panTro_q = "<STR_LIT>"<EOL>b1_tarSyr_s = "<STR_LIT>"<EOL>b1_tarSyr_q = "<STR_LIT>"<EOL>b1_tupBel_s = "<STR_LIT>"<EOL>b1_tupBel_q = "<STR_LIT>"<EOL>b1 = "<STR_LIT>" +"<STR_LIT>" + b1_hg19_seq + "<STR_LIT:\n>" +"<STR_LIT>" + b1_panTro_s + "<STR_LIT:\n>" +"<STR_LIT>" + b1_panTro_q + "<STR_LIT:\n>" +"<STR_LIT>" + "<STR_LIT:\n>" +"<STR_LIT>" + b1_tarSyr_s + "<STR_LIT:\n>" +"<STR_LIT>" + b1_tarSyr_q + "<STR_LIT:\n>" +"<STR_LIT>" + "<STR_LIT:\n>" +"<STR_LIT>" + b1_tupBel_s + "<STR_LIT:\n>" +"<STR_LIT>" + b1_tupBel_q + "<STR_LIT:\n>" +"<STR_LIT>" + "<STR_LIT:\n>" +"<STR_LIT>"<EOL>self.b1_hg19 = Sequence("<STR_LIT>", b1_hg19_seq, <NUM_LIT>, <NUM_LIT>,<EOL>"<STR_LIT:+>", <NUM_LIT>)<EOL>self.b1_panTro = Sequence("<STR_LIT>", b1_panTro_s, <NUM_LIT>, <NUM_LIT>, "<STR_LIT:+>",<EOL><NUM_LIT> - <NUM_LIT>, {QUALITY_META_KEY: b1_panTro_q,<EOL>LEFT_STATUS_KEY: "<STR_LIT:C>",<EOL>LEFT_COUNT_KEY: <NUM_LIT:0>,<EOL>RIGHT_STATUS_KEY: "<STR_LIT:C>",<EOL>RIGHT_COUNT_KEY: <NUM_LIT:0>})<EOL>self.b1_tarSyr = Sequence("<STR_LIT>", b1_tarSyr_s,<EOL><NUM_LIT> - <NUM_LIT> - <NUM_LIT:50>, <NUM_LIT> - <NUM_LIT>, "<STR_LIT:->",<EOL><NUM_LIT>, {QUALITY_META_KEY: b1_tarSyr_q,<EOL>LEFT_STATUS_KEY: "<STR_LIT:N>",<EOL>LEFT_COUNT_KEY: <NUM_LIT:0>,<EOL>RIGHT_STATUS_KEY: "<STR_LIT:C>",<EOL>RIGHT_COUNT_KEY: <NUM_LIT:0>})<EOL>self.b1_mm4 = UnknownSequence("<STR_LIT>", <NUM_LIT>, <NUM_LIT> + <NUM_LIT>, "<STR_LIT:+>",<EOL><NUM_LIT> - (<NUM_LIT> + <NUM_LIT>),<EOL>{EMPTY_ALIGNMENT_STATUS_KEY: "<STR_LIT:I>"})<EOL>b2_hg19_seq = "<STR_LIT>"<EOL>b2_panTro_s = "<STR_LIT>"<EOL>b2_panTro_q = "<STR_LIT>"<EOL>b2_tarSyr_s = "<STR_LIT>"<EOL>b2_tarSyr_q = "<STR_LIT>"<EOL>b2_tupBel_s = "<STR_LIT>"<EOL>b2_tupBel_q = "<STR_LIT>"<EOL>b2 = "<STR_LIT>" +"<STR_LIT>" + b2_hg19_seq + "<STR_LIT:\n>" +"<STR_LIT>" + b2_panTro_s + "<STR_LIT:\n>" +"<STR_LIT>" + b2_panTro_q + "<STR_LIT:\n>" +"<STR_LIT>" + "<STR_LIT:\n>" +"<STR_LIT>" + b2_tarSyr_s + "<STR_LIT:\n>" +"<STR_LIT>" + b2_tarSyr_q + "<STR_LIT:\n>" +"<STR_LIT>" + "<STR_LIT:\n>" +"<STR_LIT>" + b2_tupBel_s + "<STR_LIT:\n>" +"<STR_LIT>" + b2_tupBel_q + "<STR_LIT:\n>" +"<STR_LIT>"<EOL>self.maf1 = b1 + "<STR_LIT>" + b2<EOL>self.b2_hg19 = Sequence("<STR_LIT>", b2_hg19_seq, <NUM_LIT>, <NUM_LIT>,<EOL>"<STR_LIT:+>", <NUM_LIT>)<EOL>self.b2_panTro = Sequence("<STR_LIT>", b2_panTro_s, <NUM_LIT>, <NUM_LIT> + <NUM_LIT>,<EOL>"<STR_LIT:+>", <NUM_LIT> - (<NUM_LIT> + <NUM_LIT>),<EOL>{QUALITY_META_KEY: b2_panTro_q,<EOL>LEFT_STATUS_KEY: "<STR_LIT:C>",<EOL>LEFT_COUNT_KEY: <NUM_LIT:0>,<EOL>RIGHT_STATUS_KEY: "<STR_LIT:C>",<EOL>RIGHT_COUNT_KEY: <NUM_LIT:0>})<EOL>self.b2_tarSyr = Sequence("<STR_LIT>", b2_tarSyr_s,<EOL><NUM_LIT> - <NUM_LIT> - <NUM_LIT>, <NUM_LIT> - <NUM_LIT>, "<STR_LIT:->",<EOL><NUM_LIT>, {QUALITY_META_KEY: b2_tarSyr_q,<EOL>LEFT_STATUS_KEY: "<STR_LIT:C>",<EOL>LEFT_COUNT_KEY: <NUM_LIT:0>,<EOL>RIGHT_STATUS_KEY: "<STR_LIT:N>",<EOL>RIGHT_COUNT_KEY: <NUM_LIT:0>})<EOL>self.b1 = b1<EOL>self.b2 = b2<EOL>
Set up some MAF files to use in unit tests.