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#!/usr/bin/env python
from os import getcwd, remove, rmdir
import tempfile, shutil
from cogent.util.unit_test import TestCase, main
from cogent.app.vienna_package import RNAfold, RNAsubopt, RNAplot,\
plot_from_seq_and_struct, DataError, get_constrained_fold
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Sandra Smit", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Development"
class RNAfoldTests(TestCase):
"""Tests for the RNAfold application controller"""
def setUp(self):
self.unnamed_seq = ['AUAGCUAGCUAUGCGCUAGC','ACGGCUAUAGCUAGCGA',\
'gcuagcuauuauauaua']
self.named_seq = ['>namedseq1','AUAGCUAGCUAUGCGCUAGC','>namedseq2',\
'ACGGCUAUAGCUAGCGA']
self.mixed_seq = ['>namedseq1','AUAGCUAGCUAUGCGCUAGC',
'ACGGCUAUAGCUAGCGA','gcuagcuauuauauaua']
self.mixed_seq2 = ['>namedseq2','AUAGCUAGCUAUGCGCUAGC',
'ACGGCUAUAGCUAGCGA','gcuagcuauuauauaua']
self.temp_dir = '/tmp/test_rnafold'
def test_base_command(self):
"""RNAfold: BaseCommand should be ok for different parameter settings"""
r = RNAfold()
working_dir = getcwd()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAfold','-d1','-T','37','-S','1.07']
self.assertEqualItems(obs, exp)
r.Parameters['-noLP'].on()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAfold','-d1','-noLP','-T','37',\
'-S','1.07']
self.assertEqualItems(obs, exp)
r.Parameters['Temp'].on(15)
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAfold','-d1','-noLP','-T','15', \
'-S','1.07']
self.assertEqualItems(obs, exp)
r.Parameters['-d'].off()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAfold','-noLP','-T','15','-S','1.07']
self.assertEqualItems(obs, exp)
def test_changing_working_dir(self):
"""RNAfold: BaseCommand should be ok after changing the working dir"""
#changing in initialization
temp_dir = tempfile.mkdtemp()
r = RNAfold(WorkingDir=temp_dir)
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir))
#changing afterwards
r = RNAfold()
r.WorkingDir = temp_dir
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir))
rmdir(temp_dir)
def test_stdout(self):
"""RNAfold: StdOut should be as expected"""
r = RNAfold()
exp = '\n'.join(['>namedseq1','AUAGCUAGCUAUGCGCUAGC',\
'...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\
'...((((....)))).. ( -3.20)','GCUAGCUAUUAUAUAUA',\
'................. ( 0.00)'])+'\n'
res = r(self.mixed_seq)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
def test_stdout_input_as_path(self):
"""RNAfold: StdOut with input_as_path"""
r = RNAfold(InputHandler='_input_as_path')
f = open('/tmp/rnatestfile','w')
f.write('\n'.join(self.mixed_seq2))
f.close()
exp = '\n'.join(['>namedseq2','AUAGCUAGCUAUGCGCUAGC',\
'...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\
'...((((....)))).. ( -3.20)','GCUAGCUAUUAUAUAUA',\
'................. ( 0.00)'])+'\n'
res = r('/tmp/rnatestfile')
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
remove('/tmp/rnatestfile')
def test_stdout_input_as_path_space(self):
"""RNAfold: StdOut with input_as_path and space in filename"""
r = RNAfold(InputHandler='_input_as_path')
f = open('/tmp/rna test file','w')
f.write('\n'.join(self.mixed_seq2))
f.close()
exp = '\n'.join(['>namedseq2','AUAGCUAGCUAUGCGCUAGC',\
'...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\
'...((((....)))).. ( -3.20)','GCUAGCUAUUAUAUAUA',\
'................. ( 0.00)'])+'\n'
res = r('/tmp/rna test file')
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
remove('/tmp/rna test file')
def test_get_result_paths_unnamed_seq(self):
"""RNAfold: _get_result_paths() should work on unnamed seq"""
r = RNAfold()
res = r(self.unnamed_seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','DP'])
self.failUnless(res['DP'] is None)
self.failUnless(res['SS'] is not None)
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_get_result_paths_named_seq(self):
"""RNAfold: _get_result_paths() should work on named seq"""
r = RNAfold()
res = r(self.named_seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','DP','namedseq1_ss',\
'namedseq2_ss','namedseq1_dp','namedseq2_dp'])
res.cleanUp()
def test_get_result_paths_mixed_seq(self):
"""RNAfold: _get_result_paths() should work on partly named seq"""
r = RNAfold()
res = r(self.mixed_seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','DP','namedseq1_ss',\
'namedseq1_dp'])
res.cleanUp()
def test_get_result_paths_parameter(self):
"""RNAfold: _get_result_paths() should work with diff parameters"""
r = RNAfold()
r.Parameters['-p'].on()
res = r(self.unnamed_seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','DP'])
self.failUnless(res['DP'] is not None)
self.failUnless(res['SS'] is not None)
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_get_result_paths_working_dir(self):
"""RNAfold: _get_result_paths() should work with diff working dir"""
r = RNAfold(WorkingDir=self.temp_dir)
res = r(self.unnamed_seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','DP'])
self.failUnless(res['DP'] is None)
self.failUnless(res['SS'] is not None)
self.failUnless(isinstance(res['SS'],file))
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_get_constrained_fold_bad_data(self):
"""get_constrained_fold should handle bad data."""
test_seq = 'AAACCCGGGUUU'
constraint = '(((...)))'
#Test empty sequence.
self.assertRaises(ValueError, get_constrained_fold,\
'', constraint)
#Test empty constraint string.
self.assertRaises(ValueError, get_constrained_fold,\
test_seq, '')
#Test different length sequence and constraint.
self.assertRaises(ValueError, get_constrained_fold,\
test_seq, constraint)
def test_get_constrained_fold(self):
"""get_constrained_fold should give correct result."""
test_seq = 'AAACCCGGGUUU'
constraint = '(((......)))'
expected_struct = '((((....))))'
obs_seq, obs_struct, obs_energy = \
get_constrained_fold(test_seq,constraint)
#Test get back correct seq and struct
self.assertEqual(obs_seq, test_seq)
self.assertEqual(obs_struct, expected_struct)
def test_zzz_general_cleanup(self):
"""Executed last, clean up temp_dir"""
shutil.rmtree(self.temp_dir)
class RNAsuboptTests(TestCase):
"""Tests for the RNAsubopt application controller"""
def test_base_command(self):
"""RNAsubopt: BaseCommand should be ok for different parameter settings
"""
r = RNAsubopt()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-d2','-T','37']
self.assertEqualItems(obs, exp)
r.Parameters['-nsp'].on('GA')
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-d2','-nsp','GA',\
'-T','37']
self.assertEqualItems(obs, exp)
r.Parameters['Temp'].on(15)
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-d2','-nsp','GA',\
'-T','15']
self.assertEqualItems(obs, exp)
r.Parameters['-d'].off()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-nsp','GA','-T',\
'15']
self.assertEqualItems(obs, exp)
def test_changing_working_dir(self):
"""RNAsubopt: BaseCommand should be ok after changing the working dir
"""
temp_dir = tempfile.mkdtemp()
#changing in initialization
r = RNAsubopt(WorkingDir=temp_dir)
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
#changing afterwards
r = RNAsubopt()
r.WorkingDir = temp_dir
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
rmdir(temp_dir)
def test_stdout(self):
"""RNAsubopt: StdOut should be as expected"""
r = RNAsubopt()
seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
'ucgaucgaucagcuagcuauuauauaua']
exp = '\n'.join(
['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA -1720 100',
'.(((((((((.(((....)))....))))))))).... -16.20',
'.(((((((((((.((....)).)).))))))))).... -17.20',
'.((((((((((..((....))...)))))))))).... -16.60',
'.((((((((((.((....))....)))))))))).... -16.40',
'.(((((((((((((....)))...)))))))))).... -16.90',
'.(((((((((((.((....)).).)))))))))).... -17.20',
'UCGAUCGAUCAGCUAGCUAUUAUAUAUA 0 100',
'......(((.((....)))))....... 0.70',
'..........((....)).......... 0.60',
'..((....)).................. 0.90',
'............................ 0.00']) + '\n'
res = r(seq)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
def test_stdout_input_as_path_space(self):
"""RNAsubopt: StdOut with input_as_path and space in filename"""
mixed_seq2 = ['>namedseq2','AUAGCUAGCUAUGCGCUAGC',
'ACGGCUAUAGCUAGCGA','gcuagcuauuauauaua']
r = RNAsubopt(InputHandler='_input_as_path')
f = open('/tmp/rna test file','w')
f.write('\n'.join(mixed_seq2))
f.close()
exp = '\n'.join(['> namedseq2 [100]',
'AUAGCUAGCUAUGCGCUAGC -830 100',
'...((((((.....)))))) -8.30',
'ACGGCUAUAGCUAGCGA -320 100',
'...(((......))).. -2.30',
'...((((....)))).. -3.20',
'GCUAGCUAUUAUAUAUA 0 100',
'................. 0.00'])+'\n'
res = r('/tmp/rna test file')
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()
remove('/tmp/rna test file')
def test_get_result_paths(self):
"""RNAsubopt: _get_result_paths() should create the right dict entries
"""
r = RNAsubopt()
seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
'ucgaucgaucagcuagcuauuauauaua']
res = r(seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus'])
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
r = RNAsubopt({'-s':None,'-lodos':None,'-d':3,'-logML':None,\
'-noLP':None,'-4':None,'-noGU':None,'-noCloseGU':None})
res = r(seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus'])
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
#self.assertEqual(res['ExitStatus'],0) #platform-dependent?
res.cleanUp()
class RNAplotTests(TestCase):
"""Tests for the RNAplot application controller"""
def setUp(self):
self.unnamed_seqs = ['AUAGCUAGCUAUGCGCUAGC','...((((((.....))))))',\
'ACGGCUAUAGCUAGCGA','...((((....))))..',\
'gcuagcuauuauauaua','.................']
self.named_seqs = \
['>namedseq1','AUAGCUAGCUAUGCGCUAGC','...((((((.....))))))',\
'>namedseq2','ACGGCUAUAGCUAGCGA','...((((....))))..']
self.mixed_seqs = \
['>namedseq1','AUAGCUAGCUAUGCGCUAGC','...((((((.....))))))',\
'ACGGCUAUAGCUAGCGA','...((((....))))..',\
'gcuagcuauuauauaua','.................']
self.named_seq = \
['>namedseq','AUAGCUAGCUAUGCGCUAGC','...((((((.....))))))']
self.standard_name = 'namedseq'
self.standard_seq = 'AUAGCUAGCUAUGCGCUAGC'
self.standard_struct = '...((((((.....))))))'
self.bad_pairing_struct = '...((((((.....)))...'
self.bad_chars_struct = '...((((((.....)xx)))'
self.short_struct = '...((((((..))))))'
self.temp_dir = '/tmp/test_rnaplot'
def test_base_command(self):
"""RNAplot: BaseCommand should be ok for different parameter settings"""
r = RNAplot()
working_dir = getcwd()
self.assertEqual(r.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','RNAplot']))
r.Parameters['-t'].on(0)
self.assertEqual(r.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','RNAplot -t 0']))
r.Parameters['-o'].on('svg')
self.assertEqual(r.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','RNAplot -t 0 -o svg']))
r.Parameters['-t'].off()
self.assertEqual(r.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','RNAplot -o svg']))
def test_changing_working_dir(self):
"""RNAplot: BaseCommand should be ok after changing the working dir"""
#changing in initialization
temp_dir = tempfile.mkdtemp()
r = RNAplot(WorkingDir=temp_dir)
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAplot'%(temp_dir))
#changing afterwards
r = RNAplot()
r.WorkingDir = temp_dir
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAplot'%(temp_dir))
rmdir(temp_dir)
def test_get_result_paths_unnamed_seq(self):
"""RNAplot: _get_result_paths() should work on unnamed seq"""
r = RNAplot()
res = r(self.unnamed_seqs)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS'])
self.failUnless(res['SS'] is not None)
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_get_result_paths_named_seq(self):
"""RNAplot: _get_result_paths() should work on named seq"""
r = RNAplot()
res = r(self.named_seqs)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','namedseq1_ss',\
'namedseq2_ss'])
res.cleanUp()
def test_get_result_paths_mixed_seq(self):
"""RNAplot: _get_result_paths() should work on partly named seq"""
r = RNAplot()
res = r(self.mixed_seqs)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS','namedseq1_ss'])
res.cleanUp()
def test_get_result_paths_parameter(self):
"""RNAplot: _get_result_paths() should work with diff parameters"""
r = RNAplot()
r.Parameters['-t'].on(0)
res = r(self.unnamed_seqs)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS'])
self.failUnless(res['SS'] is not None)
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_get_result_paths_working_dir(self):
"""RNAplot: _get_result_paths() should work with diff working dir"""
r = RNAplot(WorkingDir=self.temp_dir)
res = r(self.unnamed_seqs)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus','SS'])
self.failUnless(res['SS'] is not None)
self.failUnless(isinstance(res['SS'],file))
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_rnaplot_output(self):
"""RNAplot: calling RNAplot on data should give correct result."""
r = RNAplot(WorkingDir=self.temp_dir)
res = r(self.named_seq)
ps_plot = res['namedseq_ss'].read()
observed_lines = ps_plot.split('\n')
expected_lines = RNAPLOT_RES.split('\n')
#First 8 lines depend on the runtime. Check after.
self.assertEqual(observed_lines[8:],expected_lines[8:])
res.cleanUp()
def test_plot_from_seq_and_struct_bad_data(self):
"""plot_from_seq_and_struct helper function should handle bad data.
"""
#Check bad Vienna Structure pairing
self.assertRaises(IndexError, plot_from_seq_and_struct,\
self.standard_seq, self.bad_pairing_struct)
#Check bad characters in Vienna Structure
self.assertRaises(ValueError, plot_from_seq_and_struct,\
self.standard_seq, self.bad_chars_struct)
#Check different lengths of seq and struct
self.assertRaises(DataError, plot_from_seq_and_struct,\
self.standard_seq, self.short_struct)
def test_plot_from_seq_and_struct(self):
"""plot_from_seq_and_struct helper function should give correct result.
"""
ps_plot = plot_from_seq_and_struct(self.standard_seq,\
self.standard_struct, seqname=self.standard_name)
observed_lines = ps_plot.split('\n')
expected_lines = RNAPLOT_RES.split('\n')
#First 8 lines depend on the runtime. Check after.
self.assertEqual(observed_lines[8:],expected_lines[8:])
def test_zzz_general_cleanup(self):
"""Executed last, clean up temp_dir"""
shutil.rmtree(self.temp_dir)
RNAPLOT_RES = """%!PS-Adobe-3.0 EPSF-3.0
%%Creator: PS_dot.c,v 1.38 2007/02/02 15:18:13 ivo Exp $, ViennaRNA-1.7.1
%%CreationDate: Tue Oct 21 15:44:50 2008
%%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 (\\
AUAGCUAGCUAUGCGCUAGC\\
) def
/coor [
[100.992 114.290]
[88.210 108.134]
[86.994 93.999]
[98.538 85.751]
[105.046 72.236]
[111.554 58.722]
[118.062 45.207]
[124.571 31.693]
[131.079 18.178]
[127.159 2.622]
[136.992 -10.055]
[153.034 -10.127]
[162.981 2.461]
[159.200 18.052]
[144.593 24.686]
[138.085 38.201]
[131.577 51.716]
[125.069 65.230]
[118.560 78.745]
[112.052 92.259]
] def
/pairs [
[4 20]
[5 19]
[6 18]
[7 17]
[8 16]
[9 15]
] def
init
% switch off outline pairs or bases by removing these lines
drawoutline
drawpairs
drawbases
% show it
showpage
end
%%EOF
"""
if __name__ == '__main__':
main()
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