#!/usr/bin/env python """Tests for the RNAplot parser """ from __future__ import division from cogent.util.unit_test import TestCase, main import string import re from cogent.parse.rna_plot import get_sequence, get_coordinates, get_pairs,\ RnaPlotParser __author__ = "Jeremy Widmann" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Jeremy Widmann"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "Jeremy Widmann" __email__ = "jermey.widmann@colorado.edu" __status__ = "Production" class RnaPlotParserTests(TestCase): """Tests for RnaPlotParser. """ def setUp(self): """Setup function for RnaPlotParser tests. """ self.sequence_lines = SEQUENCE_LINES.split('\n') self.expected_seq = 'AAACCGCCUUU' self.coordinate_lines = COORDINATE_LINES.split('\n') self.expected_coords = [[92.500,92.500],\ [92.500,77.500],\ [92.500,62.500],\ [82.218,50.185],\ [85.577,34.497],\ [100.000,27.472],\ [114.423,34.497],\ [117.782,50.185],\ [107.500,62.500],\ [107.500,77.500],\ [107.500,92.500]] self.pairs_lines = PAIRS_LINES.split('\n') self.expected_pairs = [[0,10],\ [1,9],\ [2,8]] self.rna_plot_lines = RNA_PLOT_FILE.split('\n') def test_get_sequence(self): """get_sequence should properly parse out sequence. """ #test real data obs_seq = get_sequence(self.sequence_lines) self.assertEqual(obs_seq, self.expected_seq) #test empty list self.assertEqual(get_sequence([]),'') def test_get_coordinates(self): """get_coordinates should proplerly parse out coordinates. """ obs_coords = get_coordinates(self.coordinate_lines) for (obs1, obs2), (exp1, exp2) in zip(obs_coords,self.expected_coords): self.assertFloatEqual(obs1,exp1) self.assertFloatEqual(obs2,exp2) #test empty list self.assertEqual(get_coordinates([]),[]) def test_get_pairs(self): """get_pairs should proplerly parse out pairs. """ obs_pairs = get_pairs(self.pairs_lines) self.assertEqual(obs_pairs, self.expected_pairs) #test empty list self.assertEqual(get_pairs([]),[]) def test_RnaPlotParser(self): """RnaPlotParser should properly parse full RNAplot postscript file. """ obs_seq, obs_coords, obs_pairs = RnaPlotParser(self.rna_plot_lines) #test seq is correctly parsed self.assertEqual(obs_seq, self.expected_seq) #test coords are correctly parsed for (obs1, obs2), (exp1, exp2) in zip(obs_coords,self.expected_coords): self.assertFloatEqual(obs1,exp1) self.assertFloatEqual(obs2,exp2) #test pairs are correctly parsed self.assertEqual(obs_pairs, self.expected_pairs) #test empty list self.assertEqual(RnaPlotParser([]),('',[],[])) SEQUENCE_LINES = """ /sequence (\ AAACCGCCUUU\ ) def /coor [ [92.500 92.500] [92.500 77.500] [92.500 62.500] [82.218 50.185] [85.577 34.497] [100.000 27.472] [114.423 34.497] [117.782 50.185] [107.500 62.500] [107.500 77.500] [107.500 92.500] ] def /pairs [ [1 11] [2 10] [3 9] ] def init % switch off outline pairs or bases by removing these lines drawoutline drawpairs drawbases % show it showpage end %%EOF """ COORDINATE_LINES = """ /coor [ [92.500 92.500] [92.500 77.500] [92.500 62.500] [82.218 50.185] [85.577 34.497] [100.000 27.472] [114.423 34.497] [117.782 50.185] [107.500 62.500] [107.500 77.500] [107.500 92.500] ] def /pairs [ [1 11] [2 10] [3 9] ] def init % switch off outline pairs or bases by removing these lines drawoutline drawpairs drawbases % show it showpage end %%EOF """ PAIRS_LINES = """ /pairs [ [1 11] [2 10] [3 9] ] def init % switch off outline pairs or bases by removing these lines drawoutline drawpairs drawbases % show it showpage end %%EOF """ RNA_PLOT_FILE = """ %!PS-Adobe-3.0 EPSF-3.0 %%Creator: PS_dot.c,v 1.38 2007/02/02 15:18:13 ivo Exp $, ViennaRNA-1.8.2 %%CreationDate: Wed Apr 14 12:08:23 2010 %%Title: RNA Secondary Structure Plot %%BoundingBox: 66 210 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: % to switch off outline pairs of sequence comment or % delete the appropriate line near the end of the file %%BeginProlog /RNAplot 100 dict def RNAplot begin /fsize 14 def /outlinecolor {0.2 setgray} bind def /paircolor {0.2 setgray} bind def /seqcolor {0 setgray} bind def /cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def /min { 2 copy gt { exch } if pop } bind def /max { 2 copy lt { exch } if pop } bind def /drawoutline { gsave outlinecolor newpath coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence currentdict /cutpoint known % check if cutpoint is defined {coor 0 cutpoint getinterval {aload pop lineto} forall % draw outline of 1st sequence coor cutpoint get aload pop 2 copy moveto 0.8 0 360 arc % draw 5' circle of 2nd sequence coor cutpoint coor length cutpoint sub getinterval {aload pop lineto} forall} % draw outline of 2nd sequence {coor {aload pop lineto} forall} % draw outline as a whole ifelse stroke grestore } bind def /drawpairs { paircolor 0.7 setlinewidth [9 3.01] 9 setdash newpath pairs {aload pop coor exch 1 sub get aload pop moveto coor exch 1 sub get aload pop lineto } forall stroke } bind def % draw bases /drawbases { [] 0 setdash seqcolor 0 coor { aload pop moveto dup sequence exch 1 getinterval cshow 1 add } forall pop } bind def /init { /Helvetica findfont fsize scalefont setfont 1 setlinejoin 1 setlinecap 0.8 setlinewidth 72 216 translate % find the coordinate range /xmax -1000 def /xmin 10000 def /ymax -1000 def /ymin 10000 def coor { aload pop dup ymin lt {dup /ymin exch def} if dup ymax gt {/ymax exch def} {pop} ifelse dup xmin lt {dup /xmin exch def} if dup xmax gt {/xmax exch def} {pop} ifelse } forall /size {xmax xmin sub ymax ymin sub max} bind def 72 6 mul size div dup scale size xmin sub xmax sub 2 div size ymin sub ymax sub 2 div translate } bind def end %%EndProlog RNAplot begin % data start here /sequence (\ AAACCGCCUUU\ ) def /coor [ [92.500 92.500] [92.500 77.500] [92.500 62.500] [82.218 50.185] [85.577 34.497] [100.000 27.472] [114.423 34.497] [117.782 50.185] [107.500 62.500] [107.500 77.500] [107.500 92.500] ] def /pairs [ [1 11] [2 10] [3 9] ] def init % switch off outline pairs or bases by removing these lines drawoutline drawpairs drawbases % show it showpage end %%EOF """ #run if called from command-line if __name__ == "__main__": main()