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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman","Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class RnaalifoldParserTest(TestCase):
"""Provides tests for RNAALIFOLD RNA secondary structure format parsers"""
def setUp(self):
"""Setup function """
#output
self.rnaalifold_out = RNAALIFOLD
#expected
self.rnaalifold_exp = [['GGCUAGGUAAAUCC',[(0,13),(1,12),(3,10)],-26.50]]
#output 2
self.rnaalifold_out_2 = RNAALIFOLD_2_STRUCTS
#expected
self.rnaalifold_exp_2 = \
[['GGCUAGGUAAAUCC',[(0,13),(1,12),(3,10)],\
float(-26.50)],\
['-GAUCCUAAGCGACGAAGUUYAWSCU------YGKRYARYRWWKKR-',\
[(6,21),(7,20),(8,19),(9,18),(10,17)],\
float(-0.80)]]
def test_rnaalifold_output(self):
"""Test for rnaalifold format parser"""
#Test empty lines
self.assertEqual(rnaalifold_parser(''),[])
#Test one structure
obs = rnaalifold_parser(self.rnaalifold_out)
self.assertEqual(obs,self.rnaalifold_exp)
#Test two structures
obs_2 = rnaalifold_parser(self.rnaalifold_out_2)
self.assertEqual(obs_2,self.rnaalifold_exp_2)
class MinimalRnaalifoldParserTest(TestCase):
"""Provides tests for MinimalRnaalifoldParser structure format parser.
"""
def setUp(self):
"""Setup function """
#output
self.rnaalifold_out = RNAALIFOLD
#expected
self.rnaalifold_exp = [['GGCUAGGUAAAUCC','((.(......).))',\
float(-26.50)]]
#output 2
self.rnaalifold_out_2 = RNAALIFOLD_2_STRUCTS
#expected
self.rnaalifold_exp_2 = \
[['GGCUAGGUAAAUCC','((.(......).))',float(-26.50)],\
['-GAUCCUAAGCGACGAAGUUYAWSCU------YGKRYARYRWWKKR-',\
'......(((((......))))).........................',\
float(-0.80)]]
def test_rnaalifold_output(self):
"""Test for rnaalifold format parser"""
#Test empty lines
self.assertEqual(MinimalRnaalifoldParser(''),[])
#Test one structure
obs = MinimalRnaalifoldParser(self.rnaalifold_out)
self.assertEqual(obs,self.rnaalifold_exp)
#Test two structures
obs_2 = MinimalRnaalifoldParser(self.rnaalifold_out_2)
self.assertEqual(obs_2,self.rnaalifold_exp_2)
RNAALIFOLD = ['GGCUAGGUAAAUCC\n',
'((.(......).)) (-26.50 = -26.50 + 0.00) \n']
RNAALIFOLD_2_STRUCTS = ['GGCUAGGUAAAUCC\n',
'((.(......).)) (-26.50 = -26.50 + 0.00) \n',\
'-GAUCCUAAGCGACGAAGUUYAWSCU------YGKRYARYRWWKKR-\n',
'......(((((......)))))......................... ( -0.80 = -1.30 + 0.50)\n',]
if __name__ == '__main__':
main()
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