#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.comrna import comRNA_parser,common
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class ComrnaParserTest(TestCase):
"""Provides tests for COMRNA RNA secondary structure format parsers"""
def setUp(self):
"""Setup function """
#output
self.comrna_out = COMRNA
#expected
self.comrna_exp = [['GGCUAGAUAGCUCA',[(0,13),(1,12),(4,9),(5,8)]],
['GGCUAGAUAGCUCA',[(0,13),(1,12),(4,9),(5,8)]],
['GGCUAGAUAGCUCA',[(0,13),(1,12),(4,9),(5,8)]],
['GGCUAGAUAGCUCA',[(0,13),(1,12)]]]
def test_comrna_output(self):
"""Test for comrna format parser"""
obs = comRNA_parser(self.comrna_out)
self.assertEqual(obs,self.comrna_exp)
def test_common_func(self):
"""Test common function in comrna parser """
obs = common(self.comrna_exp)
exp = [['GGCUAGAUAGCUCA',[(0,13),(1,12),(4,9),(5,8)]],
['GGCUAGAUAGCUCA',[(0,13),(1,12)]]]
self.assertEqual(obs,exp)
COMRNA = ['comRNA input.fasta \n', '\n', 'PARAMETERS: \n', 'L = 4, Minimum length of a straight stem;\n', 'E = -5.00, Maximum stem energy allowed for a stem to be analyzed, in kcal/mol;\n', 'S = 0.00, Minimum stem similarity score b/w two stems compared;\n', 'Sh = 0.60, Maximum stem similarity score threshold that will be tested;\n', 'Sl = 0.20, Minimum stem similarity score threshold that will be tested;\n', 'P = 0.50, Minimum percentage of sequences in which a common structure should occur;\n', 'n = 10, Number of common structures to be reported;\n', 'x = 999, Maximum number of pseudoknot crossover pattern allowed between one stem and other stems in a structure;\n', 'a = 1, Use anchor region during stem comparison;\n', 'o = 4, Maximum number of overlapping nucleotides allowed between two stems;\n', 'c = 0.30, Maximum percentage of stem length that is allowed overlapping between two stems;\n', 'j = 0.70, Maximum percentage of stems allowed overlapping between two different cliques;\n', 'r = 0.40, Minimum percentage of stems required to be same for two cliques to be considered same when reporting structures;\n', 'f = 10, Number of flanking nucleotides of a stem to be refolded together during structure refinement;\n', 'v = 5, Maximum length of nucleotides allowed for a new loop to deviate from its length in the original structure pattern;\n', 'g = 0, Use topological sort to assemble stem blocks;\n', '\n', 'Sequence file name: "input.fasta"\n', '\n', 'Sequences loaded ...\n', '1 seq1 72 nt\n', '2 seq2 72 nt\n', '3 seq3 72 nt\n', '4 seq4 72 nt\n', '\n', '\n', 'Number of stems in each energy bin for each sequence:\n', '\n', 'energy[kc/m] -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0\n', 'seq1 2 1 1 6 1 5 9 2 1 3 0 1\n', 'seq2 2 1 1 6 1 5 9 2 1 3 0 1\n', 'seq3 2 1 1 6 1 5 9 2 1 3 0 1\n', 'seq4 2 1 1 6 1 5 9 2 1 3 0 1\n', '\n', '\n', 'Pairwise Sequence Identity (%): \n', '\n', ' 1 2 3 4\n', '\n', ' 1 - 100 100 100\n', ' 2 100 - 100 100\n', ' 3 100 100 - 100\n', ' 4 100 100 100 - \n', '\n', 'Average Pairwise Sequence Identity (%): 100\n', '\n', 'Comparing stems pairwise ... \n', '\n', 'Number of edges that has stem-similarity-score higher than a certain threshold in the stem graph:\n', '\n', 'Score: 0.8 0.78 0.76 0.74 0.72 0.7 0.68 0.66 0.64 0.62 0.6 0.58 0.56 0.54 0.52 0.5 0.48 0.46 0.44 0.42 0.4 0.38 0.36 0.34 0.32 0.3 0.28 0.26 0.24 0.22 0.2\n', 'Num of edges: 12 12 18 18 18 24 24 54 72 78 102 114 114 120 132 132 144 156 168 168 174 180 180 180 180 180 180 180 180 180 180 180\n', '\n', 'Time spent on comparing stems: 0.03 seconds user CPU time; 0.04 seconds real time.\n', '\n', 'Maximum structure finding time: 1 min\n', '\n', '=========================== S = 0.6 ===========================\n', '\n', 'Find conserved stems (cliques) ... ==== 17 cliques ==== 17 unique ====\n', 'Time spent on finding conserved stems: 0 sec CPU time; 0 sec clock time.\n', '\n', 'Construct clique topological graph ... ==== 53 edges ====\n', 'Assemble conserved stems (cliques) ... ==== 44 structures ====\n', 'Time spent on topologically assembling conserved stems: 0 sec CPU time; 0 sec clock time.\n', '\n', 'Report top 10 structures.\n', '-------------------------------------------\n', 'Structure #1: Score = 10.1, pattern: 41, path: 0 1 3 , comseq: 1 2 3 4 , incompatible_seq: 0() 1() 3() \n', '(a) Clique 0: OriginalScore = 3.82, ModifiedScore = 3.82\n', ' 1, seq1 1 GGCUAGA 7 ... 66 UCUGGCC 72 [-13 kc/m]\n', ' 2, seq2 1 GGCUAGA 7 ... 66 UCUGGCC 72 [-13 kc/m]\n', ' 3, seq3 1 GGCUAGA 7 ... 66 UCUGGCC 72 [-13 kc/m]\n', ' 4, seq4 1 GGCUAGA 7 ... 66 UCUGGCC 72 [-13 kc/m]\n', '(b) Clique 1: OriginalScore = 3.45, ModifiedScore = 3.45\n', ' 1, seq1 29 GGAUUGAA 36 ... 54 UUCGAUCC 61 [-11.6 kc/m]\n', ' 2, seq2 29 GGAUUGAA 36 ... 54 UUCGAUCC 61 [-11.6 kc/m]\n', ' 3, seq3 29 GGAUUGAA 36 ... 54 UUCGAUCC 61 [-11.6 kc/m]\n', ' 4, seq4 29 GGAUUGAA 36 ... 54 UUCGAUCC 61 [-11.6 kc/m]\n', '(c) Clique 3: OriginalScore = 2.82, ModifiedScore = 2.82\n', ' 1, seq1 49 GUCGG 53 UUCGAUC 61 CCGGC 65 [-8.4 kc/m]\n', ' 2, seq2 49 GUCGG 53 UUCGAUC 61 CCGGC 65 [-8.4 kc/m]\n', ' 3, seq3 49 GUCGG 53 UUCGAUC 61 CCGGC 65 [-8.4 kc/m]\n', ' 4, seq4 49 GUCGG 53 UUCGAUC 61 CCGGC 65 [-8.4 kc/m]\n', '\n', '\n', 'seq1 1 GGCUAGAUAGCUCA 14 \n', ' aa bb bb aa\n', 'seq2 1 GGCUAGAUAGCUCA 14 \n', ' aa bb bb aa\n', 'seq3 1 GGCUAGAUAGCUCA 14 \n', ' aa bb bb aa\n', 'seq4 1 GGCUAGAUAGCUCA 14 \n', ' aa aa\n', '\n', '\n', '-------------------------------------------']
if __name__ == '__main__':
main()
