def test_multiple_repair(self): """Test repair of multiple ambiguous positions in a genome. """ repairer = AmbiguousRepair(self.ambig_info, 0) for repair_attempt in range(5): new_org = repairer.repair(self.organism) new_genome_seq = new_org.genome.toseq() assert new_genome_seq.count("*") == 0, "Did not repair genome, got %s" % str(new_genome_seq)
def test_single_repair(self): """Test repair of a single ambiguous position in a genome. """ repairer = AmbiguousRepair(self.ambig_info, 2) for repair_attempt in range(5): new_org = repairer.repair(self.organism) new_genome_seq = new_org.genome.toseq() assert new_genome_seq.data.count("*") == 2, "Did not repair genome, got %s" % new_genome_seq.data
def test_multiple_repair(self): """Test repair of multiple ambiguous positions in a genome. """ repairer = AmbiguousRepair(self.ambig_info, 0) for repair_attempt in range(5): new_org = repairer.repair(self.organism) new_genome_seq = new_org.genome.toseq() assert new_genome_seq.data.count("*") == 0, \ "Did not repair genome, got %s" % new_genome_seq.data
def test_single_repair(self): """Test repair of a single ambiguous position in a genome. """ repairer = AmbiguousRepair(self.ambig_info, 2) for repair_attempt in range(5): new_org = repairer.repair(self.organism) new_genome_seq = new_org.genome.toseq() assert new_genome_seq.count("*") == 2, \ "Did not repair genome, got %s" % new_genome_seq.tostring()