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())
