test/test_FixWidthTrack.py

   1 #!/usr/bin/env python
   2 # Time-stamp: <2019-08-09 14:19:31 taoliu>
   3
   4 import unittest
   5
   6 from MACS2.IO.FixWidthTrack import *
   7
   8 class Test_FWTrack(unittest.TestCase):
   9
  10     def setUp(self):
  11
  12         self.input_regions = [(b"chrY",0,0 ),
  13                               (b"chrY",90,0 ),
  14                               (b"chrY",150,0 ),
  15                               (b"chrY",70,0 ),
  16                               (b"chrY",80,0 ),
  17                               (b"chrY",85,0 ),
  18                               (b"chrY",85,0 ),
  19                               (b"chrY",85,0 ),
  20                               (b"chrY",85,0 ),
  21                               (b"chrY",90,1 ),
  22                               (b"chrY",150,1 ),
  23                               (b"chrY",70,1 ),
  24                               (b"chrY",80,1 ),
  25                               (b"chrY",80,1 ),
  26                               (b"chrY",80,1 ),
  27                               (b"chrY",85,1 ),
  28                               (b"chrY",90,1 ),
  29                               ]
  30         self.fw = 50
  31
  32     def test_add_loc(self):
  33         # make sure the shuffled sequence does not lose any elements
  34         fw = FWTrack(fw=self.fw)
  35         for ( c, p, s ) in self.input_regions:
  36             fw.add_loc(c, p, s)
  37         fw.finalize()
  38         # roughly check the numbers...
  39         self.assertEqual( fw.total, 17 )
  40         self.assertEqual( fw.length, 17*self.fw )
  41
  42     def test_filter_dup(self):
  43         # make sure the shuffled sequence does not lose any elements
  44         fw = FWTrack(fw=self.fw)
  45         for ( c, p, s ) in self.input_regions:
  46             fw.add_loc(c, p, s)
  47         fw.finalize()
  48         # roughly check the numbers...
  49         self.assertEqual( fw.total, 17 )
  50         self.assertEqual( fw.length, 17*self.fw )
  51
  52         # filter out more than 3 tags
  53         fw.filter_dup( 3 )
  54         # one chrY:85:0 should be removed
  55         self.assertEqual( fw.total, 16 )
  56
  57         # filter out more than 2 tags
  58         fw.filter_dup( 2 )
  59         # then, one chrY:85:0 and one chrY:80:- should be removed
  60         self.assertEqual( fw.total, 14 )
  61
  62         # filter out more than 1 tag
  63         fw.filter_dup( 1 )
  64         # then, one chrY:85:0 and one chrY:80:1, one chrY:90:1 should be removed
  65         self.assertEqual( fw.total, 11 )
  66
  67
  68     def test_sample_num(self):
  69         # make sure the shuffled sequence does not lose any elements
  70         fw = FWTrack(fw=self.fw)
  71         for ( c, p, s ) in self.input_regions:
  72             fw.add_loc(c, p, s)
  73         fw.finalize()
  74         # roughly check the numbers...
  75         self.assertEqual( fw.total, 17 )
  76         self.assertEqual( fw.length, 17*self.fw )
  77
  78         fw.sample_num( 10 )
  79         self.assertEqual( fw.total, 9 )
  80
  81     def test_sample_percent(self):
  82         # make sure the shuffled sequence does not lose any elements
  83         fw = FWTrack(fw=self.fw)
  84         for ( c, p, s ) in self.input_regions:
  85             fw.add_loc(c, p, s)
  86         fw.finalize()
  87         # roughly check the numbers...
  88         self.assertEqual( fw.total, 17 )
  89         self.assertEqual( fw.length, 17*self.fw )
  90
  91         fw.sample_percent( 0.5 )
  92         self.assertEqual( fw.total, 8 )
  93