Source Code for Module dimer.genome.bedops_tests

 1  import sys, os, random 
 2  import unittest 
 3  import tempfile 
 4  from operator import itemgetter 
 5  from functools import partial 
 6   
 7  try: 
 8      sys.path.insert(0, os.path.dirname(os.path.dirname(__file__))) 
 9  except: 
10      sys.path.insert(0, os.path.dirname(os.path.abspath("."))) 
11   
12  from bedops import bedmap, overlap_as_array 
13  from . import parseBED 
14   
15 -class TestBEDMAP(unittest.TestCase): 
16 -    def setUp(self): 
17          if not ( hasattr(self, "anchor_fn") and os.path.exists(self.anchor_fn) ): 
18              with tempfile.NamedTemporaryFile(delete=False) as rfd: 
19                  rfd.write("\n".join( ("chr1\t10\t100\ta1\t1.3\t+", 
20                          "chr1\t200\t290\ta2\t22.2\t+", 
21                          "chr4\t5\t95\ta3\t43.5\t-\n") )) 
22                  self.anchors = rfd.name 
23   
24          if not ( hasattr(self, "t1") and os.path.exists(self.t1) ): 
25              with tempfile.NamedTemporaryFile(delete=False) as mfd: 
26                  mfd.write("\n".join( ("chr1\t15\t30\tt11\t1", 
27                          "chr1\t25\t30\tmp2\t0.5", 
28                          "chr3\t55\t80\tmp2\t1", 
29                          "chr4\t20\t56\tmp3\t23.3\n") )) 
30                  self.t1 = mfd.name 
31          self.anchor_len = 90 
32          self.B = random.choice((1, 2, 3, 5, 6, 9)) 
33          self.B = 5 
34   
35 -    def test_bedmap(self): 
36          original_anchors = map(parseBED, open(self.anchors)) 
37          bdemp_res = list( bedmap(self.anchors, self.t1, onlyOverlapping=False) ) 
38   
39          self.assertTrue( all( map(lambda a: a[2]-a[1] == self.anchor_len, original_anchors) ) ) 
40          self.assertEqual( original_anchors, map(parseBED, map(itemgetter(0), bdemp_res)) ) 
41   
42          for anchor_str, ft_str in bdemp_res: 
43              anchor = parseBED(anchor_str) 
44              ft_lst = map(parseBED, filter(bool, ft_str.split(";"))) 
45   
46              #all fatures it into anchor 
47              self.assertTrue( all( map(lambda ft: max(ft[1], anchor[1]) < min(ft[2], anchor[2]), ft_lst) ) ) 
48   
49              x_s = overlap_as_array(anchor, ft_str.split(";"), bin=self.B, parseFeature=partial(parseBED, use_score=True)) 
50              x_c = overlap_as_array(anchor, ft_str.split(";"), bin=self.B, parseFeature=partial(parseBED, use_score=False)) 
51   
52              #print anchor 
53              #print self.B 
54              print x_c 
55              #print x_s 
56              if anchor[5] == "-": 
57                  print ft_lst 
58                  ft_lst = map(lambda (_ch, _s, _e, _n, _sc): (_ch, anchor[1]+anchor[2]-_e, anchor[2]+anchor[1]-_s, _n, _sc), ft_lst) 
59                  print ft_lst 
60                  print 
61   
62              self.assertEqual( x_s.shape[0], x_c.shape[0] ) 
63              for i in range(x_c.shape[0]): 
64                  s = anchor[1] + self.B*i 
65                  e = anchor[1] + self.B*(i+1) 
66   
67                  sel_feats = filter(lambda f: max(s, f[1]) < min(e, f[2]), ft_lst) 
68                  overlap = map(lambda f: min(e, f[2]) - max(s, f[1]), sel_feats) 
69                  if anchor[5] == "-": 
70                      print i, s, e, sel_feats, overlap 
71                  score = map(itemgetter(4), sel_feats) 
72   
73   
74                  self.assertEqual( sum(overlap), x_c[i] ) 
75                  self.assertAlmostEqual( x_s[i], sum( map(lambda (s,o): s*o, zip(score, overlap)) ), places=4 ) 
76   
77   
78   
79   
80  if __name__ == '__main__': 
81      unittest.main() 
82