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