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#!/usr/bin/env python
"""Tests for the RNAfold dot plot parser
"""
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.parse.rna_fold import *
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Production"
class RnaFoldParserTests(TestCase):
"""Tests for RnaFoldParser.
"""
def setUp(self):
"""Setup function for RnaFoldParser tests.
"""
self.rna_fold_parser_results = ('ACGUGCUAG',
[(1, 7, float(0.01462)),
(2, 9, float(0.11118)),
(3, 7, float(0.00985)),
(4, 8, float(0.01005)),
(4, 9, float(0.01586))])
self.sequence_lines = ['/sequence line before where sequences start\n',
' ACCUGUCUAUCGCUGC&*$#@(*\n',
'ACGGUUAUAUUAUCUCUG\\\n',
') end of sequence\n']
self.sequence_lines_empty = ['/sequence \n',
'\n',
')\n']
self.index_lines = ['unimportant line',
'1 3 0.332 ubox',
'1 4 0.003 ubox']
self.index_lines_no_ubox = ['unimportant line',
'1 2 0.432 u box',
'1 4 0.32 ubo x']
def test_getSequence(self):
self.assertEqual(getSequence(self.sequence_lines),
'ACCUGUCUAUCGCUGC&*$#@(*ACGGUUAUAUUAUCUCUG')
self.assertEqual(getSequence(self.sequence_lines_empty),'')
def test_getIndices(self):
self.assertEqual(getIndices(self.index_lines),[(1,3,float(0.332)),
(1,4,float(0.003))])
self.assertEqual(getIndices(self.index_lines_no_ubox),[])
def test_RnaFoldParser(self):
self.assertEqual(RnaFoldParser([]), ('',[]))
self.assertEqual(RnaFoldParser(RNA_FOLD_RESULTS),
self.rna_fold_parser_results)
RNA_FOLD_RESULTS = ['%!PS-Adobe-3.0 EPSF-3.0\n',
'%%Title: RNA DotPlot\n',
'%%Creator: PS_dot.c,v 1.24 2003/08/07 09:01:00 ivo Exp $, ViennaRNA-1.5\n',
'%%CreationDate: Fri Oct 8 13:15:01 2004\n',
'%%BoundingBox: 66 211 518 662\n',
'%%DocumentFonts: Helvetica\n',
'%%Pages: 1\n',
'%%EndComments\n',
'\n',
'%Options: \n',
'%This file contains the square roots of the base pair probabilities in the form\n',
'% i j sqrt(p(i,j)) ubox\n',
'100 dict begin\n',
'\n',
'/logscale false def\n',
'\n',
'%delete next line to get rid of title\n',
'270 665 moveto /Helvetica findfont 14 scalefont setfont (dot.ps) show\n',
'\n',
'/lpmin {\n',
' 1e-05 log % log(pmin) only probs>pmin will be shown\n',
'} bind def\n',
'\n',
'/box { %size x y box - draws box centered on x,y\n',
' 2 index 0.5 mul add % x += 0.5\n',
' exch 2 index 0.5 mul add exch % x += 0.5\n',
' newpath\n',
' moveto\n',
' dup neg 0 rlineto\n',
' dup neg 0 exch rlineto\n',
' 0 rlineto\n',
' closepath\n',
' fill\n',
'} bind def\n',
'\n',
'/sequence { (\\\n',
'ACGUGCUAG\\\n',
') } def\n',
'/len { sequence length } bind def\n',
'\n',
'/ubox {\n',
' logscale {\n',
' log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if\n',
' } if\n',
' 3 1 roll\n',
' exch len exch sub 1 add box\n',
'} bind def\n',
'\n',
'/lbox {\n',
' 3 1 roll\n',
' len exch sub 1 add box\n',
'} bind def\n',
'\n',
'72 216 translate\n',
'72 6 mul len 1 add div dup scale\n',
'/Helvetica findfont 0.95 scalefont setfont\n',
'\n',
'% print sequence along all 4 sides\n',
'[ [0.7 -0.3 0 ]\n',
' [0.7 0.7 len add 0]\n',
' [0.7 -0.2 90]\n',
' [-0.3 len sub 0.7 len add -90]\n',
'] {\n',
' gsave\n',
' aload pop rotate translate\n',
' 0 1 len 1 sub {\n',
' dup 0 moveto\n',
' sequence exch 1 getinterval\n',
' show\n',
' } for\n',
' grestore\n',
'} forall\n',
'\n',
'0.5 dup translate\n',
'% draw diagonal\n',
'0.04 setlinewidth\n',
'0 len moveto len 0 lineto stroke \n',
'\n',
'%draw grid\n',
'0.01 setlinewidth\n',
'len log 0.9 sub cvi 10 exch exp % grid spacing\n',
'dup 1 gt {\n',
' dup dup 20 div dup 2 array astore exch 40 div setdash\n',
'} { [0.3 0.7] 0.1 setdash } ifelse\n',
'0 exch len {\n',
' dup dup\n',
' 0 moveto\n',
' len lineto \n',
' dup\n',
' len exch sub 0 exch moveto\n',
' len exch len exch sub lineto\n',
' stroke\n',
'} for\n',
'0.5 neg dup translate\n',
'\n',
'1 7 0.01462 ubox\n',
'2 9 0.11118 ubox\n',
'3 7 0.00985 ubox\n',
'4 8 0.01005 ubox\n',
'4 9 0.01586 ubox\n',
'showpage\n',
'end\n',
'%%EOF\n']
#run if called from command-line
if __name__ == "__main__":
main()
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