def setUp(self):
<EOL>head_l1 = "<STR_LIT>" +"<STR_LIT>"<EOL>head_l2 = "<STR_LIT>" +"<STR_LIT>"<EOL>an1 = "<STR_LIT>"<EOL>an2 = "<STR_LIT>" +"<STR_LIT>"<EOL>an3 = "<STR_LIT>" +"<STR_LIT>"<EOL>an4 = "<STR_LIT>" +"<STR_LIT>"<EOL>an5 = "<STR_LIT>" +"<STR_LIT>"<EOL>an6 = "<STR_LIT>" +"<STR_LIT>"<EOL>self.ann = (head_l1 + "<STR_LIT:\n>" + head_l2 + "<STR_LIT>" + an1 + "<STR_LIT:\n>" + an2 + "<STR_LIT:\n>" +<EOL>an3 + "<STR_LIT:\n>" + an4 + "<STR_LIT:\n>" + an5 + "<STR_LIT:\n>" + an6)<EOL>self.indv_an = [an1, an2, an3, an4, an5, an6]<EOL>alig_1_header = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_1 = "<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>"<EOL>alig_1_m = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_2_header = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_2 = "<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>"<EOL>alig_2_m = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_3_header = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_3 = "<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>"<EOL>alig_3_m = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_4_header = "<STR_LIT>" +"<STR_LIT>"<EOL>alig_4 = "<STR_LIT>" +"<STR_LIT>" +"<STR_LIT>"<EOL>alig_4_m = "<STR_LIT>"<EOL>self.rm_tc1_records = [alig_1_header + "<STR_LIT>" + alig_1 + "<STR_LIT>" + alig_1_m,<EOL>alig_2_header + "<STR_LIT>" + alig_2 + "<STR_LIT>" + alig_2_m,<EOL>alig_3_header + "<STR_LIT>" + alig_3 + "<STR_LIT>" + alig_3_m,<EOL>alig_4_header + "<STR_LIT>" + alig_4 + "<STR_LIT>" + alig_4_m]<EOL>self.rm_rc_1_input = "<STR_LIT>".join(self.rm_tc1_records)<EOL>
Set up some data to use in tests; create a repeatmasker annotation file
and a corresponding full alignment file.