1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
|
#!/usr/bin/env python
"""This script/module can do any of 5 different actions with the figures it makes.
When run as a script, one of the actions must be specified:
- exercise
The default when used as a module. Drawing code is used to make a
matplotlib figure object but that is all.
- record
Save PNG images of the figures in draw_results/baseline/
To be used before making changes in drawing code.
- check
Compare figures with saved baseline figures. Fail if they don't match.
Failed figures are saved in draw_results/current. Also makes an HTML
page comparing them with the baseline images.
- compare
Save ALL differing figures in draw_results/current and make HTML page
comparing them with the baseline images.
- view
Save all differing figures in draw_results/current and make HTML page
comparing them with the baseline images, along with all the matching
figures too.
"""
import warnings
warnings.filterwarnings('ignore', category=UserWarning, module='matplotlib')
import matplotlib
matplotlib.use('Agg')
import unittest
import sys, os, cStringIO
from cogent import DNA, LoadTree, LoadSeqs
from cogent.core import alignment, alphabet, annotation
from cogent.draw.linear import *
from cogent.draw.dendrogram import *
from cogent.draw.compatibility import partimatrix
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",
"Matthew Wakefield"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def file_for_test(msg, baseline=False, prefixed=True):
file_ext = "png"
dirname = 'baseline' if baseline else 'current'
if prefixed:
dirname = os.path.join('draw_results', dirname)
fname = msg.replace(' ', '_') + '.' + file_ext
return os.path.join(dirname, fname)
def fig2png(fig):
f = cStringIO.StringIO()
fig.savefig(f, format='png')
return f.getvalue()
def writefile(fname, content):
dirname = os.path.dirname(fname)
if not os.path.exists(dirname):
os.makedirs(dirname)
f = open(fname, 'wb')
f.write(content)
f.close()
def exercise(msg, fig):
pass
def record(msg, fig):
png = fig2png(fig)
fname = file_for_test(msg, True)
writefile(fname, png)
class CheckOutput(object):
def __init__(self, failOnDifference=True, showAll=False):
if not os.path.exists('draw_results/baseline'):
raise RuntimeError(
'No baseline found. Run "test_draw.py record" first')
self.results = []
self.failOnDifference = failOnDifference
self.showAll = showAll
self.anyFailures = False
def __call__(self, msg, fig):
fname = file_for_test(msg, True)
observed = fig2png(fig)
if os.path.exists(fname):
expected = open(fname, 'rb').read()
different = observed != expected
self.results.append((msg, different))
if different:
self.anyFailures = True
writefile(file_for_test(msg, False), observed)
if self.failOnDifference:
raise AssertionError('See draw_results/comparison.html')
else:
print 'difference from', fname
else:
raise RuntimeError('No baseline image at %s' % fname)
def writeHTML(self):
html = ['<html><head><title>Drawing Test Output</title></head>',
'<body>']
html.append('<p>%s figures of which %s differ from baseline' % (
len(self.results), sum(d for (m,d) in self.results)))
for (msg, different) in self.results:
fn1 = file_for_test(msg, True, False)
fn2 = file_for_test(msg, False, False)
if different:
html.append('<h2>%s</h2>' % msg)
html.append('<h3>Old</h3>')
html.append('<img src="%s"/>' % fn1)
html.append('<h3>New</h3>')
html.append('<img src="%s"/>' % fn2)
elif self.showAll:
html.append('<h2>%s</h2>' % msg)
html.append('<img src="%s"/>' % fn1)
else:
html.append('<p>%s</p>' % msg)
html.append('<hr/>')
html.append('</body></html>')
html = '\n'.join(html)
f = open('draw_results/comparison.html', 'w')
f.write(html)
f.close()
def report(self):
self.writeHTML()
if self.anyFailures or self.showAll:
if sys.platform == 'darwin':
import subprocess
subprocess.call(['open', 'draw_results/comparison.html'])
else:
print "See draw_results/comparison.html"
def do(msg, display, **kw):
fig = display.makeFigure(**kw)
test_figure(msg, fig)
def makeSampleSequence():
seq = 'tgccnwsrygagcgtgttaaacaatggccaactctctaccttcctatgttaaacaagtgagatcgcaggcgcgccaaggc'
seq = DNA.makeSequence(seq)
v = seq.addAnnotation(annotation.Feature, 'exon', 'exon', [(20,35)])
v = seq.addAnnotation(annotation.Feature, 'repeat_unit', 'repeat_unit', [(39,49)])
v = seq.addAnnotation(annotation.Feature, 'repeat_unit', 'rep2', [(49,60)])
return seq
def makeSampleAlignment():
# must be an esier way to make an alignment of annotated sequences!
from cogent.align.align import global_pairwise, make_dna_scoring_dict
DNA = make_dna_scoring_dict(10, -8, -8)
seq1 = makeSampleSequence()[:-2]
seq2 = makeSampleSequence()[2:]
seq2 = seq2[:30] + seq2[50:]
seq1.Name = 'FAKE01'
seq2.Name = 'FAKE02'
names = (seq1.getName(), seq2.getName())
align = global_pairwise(seq1, seq2, DNA, 2, 1)
align.addAnnotation(annotation.Variable, 'redline', 'align', [((0,15),1),((15,30),2),((30,45),3)])
align.addAnnotation(annotation.Variable, 'blueline', 'align', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])
return align
seq = makeSampleSequence()
a = seq.addAnnotation(annotation.Variable, 'blueline', 'seq', [((0,15),1),((15,30),2),((30,45),3)])
v = seq.addAnnotation(annotation.Feature, 'gene', 'gene', [(0,15),(20,35),(40,55)])
b = v.addAnnotation(annotation.Variable, 'redline', 'feat', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])
align = makeSampleAlignment()
def green_cg(seq):
seq = str(seq)
posn = 0
result = []
while True:
last = posn
posn = seq.find('CG', posn)
if posn < 0: break
result.append('k' * (posn-last)+'gg')
posn += 2
result.append('k' * (len(seq)-last))
return list(''.join(result))
class DrawingTests(unittest.TestCase):
def test_seqs(self):
seqd = Display(seq)
do('sequence wrapped at 50',
seqd, rowlen=50)
small = FontProperties(size=7, stretch='extra-condensed')
do('squashed sequence',
seqd.copy(seq_font=small, colour_sequences=True))
do('seq display slice from 5 to 45 starts %s' % seq[5:8],
seqd[5:45])
def test_alns(self):
alignd = Display(align, colour_sequences=True, min_feature_height=10)
do('coloured text alignment',
alignd)
do('coloured alignment no text',
alignd.copy(show_text=False))
do('no text and no colour',
alignd.copy(show_text=False, colour_sequences=False))
do('no shapes',
alignd.copy(show_text=False, draw_bases=False))
do('no text or colour or shapes',
alignd.copy(show_text=False, colour_sequences=False, draw_bases=False))
do('green seqs',
alignd.copy(seq_color_callback=green_cg))
def test_legend(self):
from cogent.draw.legend import Legend
do('Feature Legend', Legend())
def test_dotplot(self):
from cogent.draw.dotplot import Display2D
do('2d', Display2D(seq, seq[:40], show_text=False, draw_bases=False))
def test_trees(self):
treestring = "((A:.1,B:.22)ab:.3,((C:.4,D:.5)cd:.55,E:.6)cde:.7,F:.2)"
for edge in 'ABCDEF':
treestring = treestring.replace(edge, edge+edge.lower()*10)
t = LoadTree(treestring=treestring)
for klass in [
UnrootedDendrogram,
SquareDendrogram,
ContemporaneousDendrogram,
ShelvedDendrogram,
# StraightDendrogram,
# ContemporaneousStraightDendrogram
]:
dendro = klass(t)
dendro.getConnectingNode('Ccccccccccc', 'Eeeeeeeeeee').setCollapsed(
color="green", label="C, D and E")
do(klass.__name__, dendro, shade_param="length",
show_params=["length"])
def callback(edge):
return ["blue", "red"][edge.Name.startswith("A")]
do("Highlight edge A", UnrootedDendrogram(t), edge_color_callback=callback)
def test_partimatrix(self):
aln = LoadSeqs(filename='data/brca1.fasta', moltype=DNA)
species5 = ['Human','HowlerMon','Mouse','NineBande','DogFaced']
aln = aln.takeSeqs(species5)
aln = aln[:500]
fig = partimatrix(aln, samples=0, display=True, print_stats=False,
s_limit=10, title="brca1")
test_figure('compatibility', fig)
if __name__ != "__main__":
test_figure = exercise
else:
myargs = []
for arg in ['exercise', 'record', 'check', 'compare', 'view']:
if arg in sys.argv:
sys.argv.remove(arg)
myargs.append(arg)
if len(myargs) != 1:
print 'Need one action, got', myargs
print __doc__
sys.exit(1)
action = myargs[0]
if action == 'record':
test_figure = record
elif action == 'check':
test_figure = CheckOutput(True)
elif action == 'compare':
test_figure = CheckOutput(False)
elif action == 'view':
test_figure = CheckOutput(False, True)
elif action == 'exercise':
test_figure = exercise
else:
raise RuntimeError('Unknown action %s' % action)
try:
unittest.main()
finally:
if hasattr(test_figure, 'report'):
test_figure.report()
|
