def test_signaturs_large_genome(self): f = fileinput.input(os.path.join(data_path,"8M_genome.fna")) c= list(SeqIO.parse(f,"fasta")) f.close dna_c = dna.DNA(id = c[0].id, seq = str(c[0].seq)) dna_c.calculate_signature() calculated_parameters = ml.fit_parameters([dna_c]) assert_equal(len(calculated_parameters), 136)
def test_parameters_one_contig_basic(self): f = fileinput.input(os.path.join(data_path,"bambus2.scaffold.linear.fasta.one_contig")) c = list(SeqIO.parse(f,"fasta")) f.close() dna_c = dna.DNA(id = c[0].id, seq = str(c[0].seq)) dna_c.calculate_signature() c_sig = self.CORRECT_SIGNATURES_ONE_CONTIG n = sum(c_sig.values()) correct_parameters = np.zeros(dna.DNA.kmer_hash_count) for i,v in c_sig.iteritems(): correct_parameters[i] += v correct_parameters/=np.sum(correct_parameters) calculated_parameters = ml.fit_parameters([dna_c]) assert_equal(calculated_parameters[0],correct_parameters[0]) assert_equal((calculated_parameters==correct_parameters).all(),True)