def test_to_file(self):
st = StockholmAlignment(self.seqs, gc=self.GC, gf=self.GF, gs=self.GS,
gr=self.GR)
with tempfile.NamedTemporaryFile('r+') as temp_file:
st.to_file(temp_file)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
exp = ('# STOCKHOLM 1.0\n'
'#=GF AC RF00360\n'
'#=GF BM cmbuild -F CM SEED\n'
'#=GF BM cmsearch -Z 274931 -E 1000000\n'
'#=GF SQ 9\n'
'#=GF RN [1]\n'
'#=GF RM 11469857\n'
'#=GF RT TITLE1\n'
'#=GF RA Auth1;\n'
'#=GF RL J Mol Biol\n'
'#=GF RN [2]\n'
'#=GF RM 12007400\n'
'#=GF RT TITLE2\n'
'#=GF RA Auth2;\n'
'#=GF RL Cell\n'
'#=GS seq1 AC 111\n'
'#=GS seq2 AC 222\n'
'seq1 ACC-G-GGTA\n'
'#=GR seq1 SS 1110101111\n'
'seq2 TCC-G-GGCA\n'
'#=GR seq2 SS 0110101110\n'
'#=GC SS_cons (((....)))\n//')
self.assertEqual(obs, exp)
def test_to_file(self):
st = StockholmAlignment(self.seqs, gc=self.GC, gf=self.GF, gs=self.GS,
gr=self.GR)
with tempfile.NamedTemporaryFile('r+') as temp_file:
st.to_file(temp_file)
temp_file.flush()
temp_file.seek(0)
obs = temp_file.read()
exp = ('# STOCKHOLM 1.0\n'
'#=GF AC RF00360\n'
'#=GF BM cmbuild -F CM SEED\n'
'#=GF BM cmsearch -Z 274931 -E 1000000\n'
'#=GF SQ 9\n'
'#=GF RN [1]\n'
'#=GF RM 11469857\n'
'#=GF RT TITLE1\n'
'#=GF RA Auth1;\n'
'#=GF RL J Mol Biol\n'
'#=GF RN [2]\n'
'#=GF RM 12007400\n'
'#=GF RT TITLE2\n'
'#=GF RA Auth2;\n'
'#=GF RL Cell\n'
'#=GS seq1 AC 111\n'
'#=GS seq2 AC 222\n'
'seq1 ACC-G-GGTA\n'
'#=GR seq1 SS 1110101111\n'
'seq2 TCC-G-GGCA\n'
'#=GR seq2 SS 0110101110\n'
'#=GC SS_cons (((....)))\n//')
self.assertEqual(obs, exp)
