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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.rnaforester import rnaforester_parser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class RnaforesterParserTest(TestCase):
"""Provides tests for RNAforester RNA secondary structure format parsers"""
def setUp(self):
"""Setup function
application output is not always actual(real) output from
the application but output in the format of the application
output in question. this to save space and time(mine)"""
#output
self.rnaforester_out = RNAFORESTER
#expected
self.rnaforester_exp = [[{'seq1':'ggccacguagcucagucgguagagcaaaggacugaaaauccuugugucguugguucaauuccaaccguggccacca',
'seq2':'-gccagauagcucagucgguagagcguucgccugaaaagugaaaggucgccgguucgaucccggcucuggccacca'},
'ggccacauagcucagucgguagagcaaacgacugaaaagccaaaggucgccgguucaaucccaacccuggccacca',
[(0, 71), (1, 70), (2, 69), (3, 68), (4, 67), (5, 66), (6, 65), (9, 24),
(10, 23), (11, 22), (12, 21), (26, 42), (27, 41), (28, 40), (29, 39),
(31, 38), (32, 37), (48, 64), (49, 63), (50, 62), (51, 61), (52, 60)]]]
def test_rnaforester_output(self):
"""Test for rnaforester format"""
obs = rnaforester_parser(self.rnaforester_out)
self.assertEqual(obs,self.rnaforester_exp)
RNAFORESTER = ['*** Scoring parameters ***\n', '\n',
'Scoring type: similarity\n', 'Scoring parameters:\n', 'pm: 10\n',
'pd: -5\n', 'bm: 1\n', 'br: 0\n', 'bd: -10\n', '\n', '\n',
'Input string (upper or lower case); & to end for multiple alignments, @ to quit\n',
'....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8\n',
'\n', '*** Calculation ***\n', '\n', 'clustering threshold is: 0.7\n',
'join clusters cutoff is: 0\n', '\n', 'Computing all pairwise similarities\n',
'2,1: 0.74606\n', '\n', 'joining alignments:\n', '1,2: 0.74606 -> 1\n',
'Calculate similarities to other clusters\n', '\n', '\n', '*** Results ***\n',
'\n', 'Minimum basepair probability for consensus structure (-cmin): 0.5\n',
'\n', 'RNA Structure Cluster Nr: 1\n', 'Score: 264.25\n', 'Members: 2\n', '\n', 'seq1 ggccacguagcucagucgguagagcaaaggacugaaaauccuugugucguugguu\n',
'seq2 -gccagauagcucagucgguagagcguucgccugaaaagugaaaggucgccgguu\n',
' **** ****************** * ******* **** ****\n', '\n',
'seq1 caauuccaaccguggccacca\n',
'seq2 cgaucccggcucuggccacca\n',
' * ** ** * *********\n', '\n',
'seq1 (((((((..((((........)))).(((((.......))))).....(((((..\n',
'seq2 -((((((..((((........)))).((((.((....)))))).....(((((..\n',
' ***************************** **** *****************\n', '\n', 'seq1 .....))))))))))))....\n',
'seq2 .....))))))))))).....\n',
' **************** ****\n', '\n', '\n',
'Consensus sequence/structure:\n',
' 100% **** ****************** * ******* **** ****\n', ' 90% **** ****************** * ******* **** ****\n', ' 80% **** ****************** * ******* **** ****\n', ' 70% **** ****************** * ******* **** ****\n', ' 60% **** ****************** * ******* **** ****\n', ' 50% *******************************************************\n', ' 40% *******************************************************\n', ' 30% *******************************************************\n', ' 20% *******************************************************\n', ' 10% *******************************************************\n', ' ggccacauagcucagucgguagagcaaacgacugaaaagccaaaggucgccgguu\n', ' (((((((..((((........)))).((((.((....)))))).....(((((..\n', ' 10% *******************************************************\n', ' 20% *******************************************************\n', ' 30% *******************************************************\n', ' 40% *******************************************************\n', ' 50% *******************************************************\n', ' 60% *******************************************************\n', ' 70% ****************************** **** ****************\n', ' 80% ****************************** **** ****************\n', ' 90% ****************************** **** ****************\n', ' 100% ****************************** **** ****************\n', '\n', ' 100% * ** ** * *********\n', ' 90% * ** ** * *********\n', ' 80% * ** ** * *********\n', ' 70% * ** ** * *********\n', ' 60% * ** ** * *********\n', ' 50% *********************\n', ' 40% *********************\n', ' 30% *********************\n', ' 20% *********************\n', ' 10% *********************\n', ' caaucccaacccuggccacca\n', ' .....))))))))))))....\n', ' 10% *********************\n', ' 20% *********************\n', ' 30% *********************\n', ' 40% *********************\n', ' 50% *********************\n', ' 60% *********************\n', ' 70% **************** ****\n', ' 80% **************** ****\n', ' 90% **************** ****\n', ' 100% **************** ****\n', '\n', '\n']
if __name__ == '__main__':
main()
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