def test_generate_contigs_of_length_4(self): with tempfile.NamedTemporaryFile() as tmp_file: tmp_file.write(self.TWO_GENOMES) tmp_file.seek(0) seqs = generate_contigs.get_sequences(tmp_file) contigs = generate_contigs.get_contigs(seqs,4) for k,v in contigs.iteritems(): for i in range(len(v)): v[i] = str(v[i]) assert_equal({"genome1":["GGGG","CCCC","TTTT","TAAA","ATTA","TATG","CGCG","CGCA","ACAC"], "genome2":["ATTA","TATA","TGAG","AGCG","CGCG","CGGT","GTGT","CTCT","GCTG"]}, contigs)
def test_write_to_fasta(self): with tempfile.NamedTemporaryFile() as tmp_file: tmp_file.write(self.TWO_GENOMES) tmp_file.seek(0) seqs = generate_contigs.get_sequences(tmp_file) contigs = generate_contigs.get_contigs(seqs,4) with tempfile.NamedTemporaryFile() as tmp_file: generate_contigs.write_sequences(contigs,tmp_file) tmp_file.seek(0) assert_equal(self.OUTPUT_CONTIGS,tmp_file.read())
def test_get_two_genomes(self): with tempfile.NamedTemporaryFile() as tmp_file: tmp_file.write(self.TWO_GENOMES) tmp_file.seek(0) assert_equal(2,len(generate_contigs.get_sequences(tmp_file) ))