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()