def test_sample_contig2(self):
s_set = SampleSetting("genomes",1000,\
1200,1200,\
False)
dir = os.path.dirname(__file__)
dna_file = os.path.join(dir,"fixtures/8M_genome.fna")
genome_seq = list(SeqIO.parse(dna_file, "fasta"))
genome = dna.DNA(id="test01", seq=str(genome_seq[0].seq))
contig = sample_contig(genome,s_set,1)
assert_equal(len(contig.full_seq),1200)
assert_equal(contig.id, 'test01 contig')
def test_genome(self, genome_index):
score_objs = []
i = 0
genome = self.group.genomes[genome_index]
while i < self.count_per_g[genome_index]:
c = sample_contig(genome, self.x_st, self.id_gen.id())
c.calculate_signature()
new_par = par_subtraction(copy(genome.signature),c)
score_obj = score_contig(c, new_par, genome, genome_index, self)
score_objs.append(score_obj)
i+=1
return score_objs