test/test_PeakIO.py

   1 #!/usr/bin/env python
   2 # Time-stamp: <2022-09-14 13:33:37 Tao Liu>
   3
   4 import unittest
   5 import sys
   6
   7 from MACS3.IO.PeakIO import *
   8
   9 class Test_PeakIO(unittest.TestCase):
  10     def setUp(self):
  11         self.test_peaks1 = [  (b"chrY",0,100),
  12                               (b"chrY",300,500),
  13                               (b"chrY",700,900),
  14                               (b"chrY",1000,1200),
  15                               (b"chrY",1250,1450),
  16                               (b"chrX",1000,2000),
  17                               (b"chrX",3000,4000),
  18                               (b"chr1",100, 10000), # chr1 only has one region but overlapping with peaks2
  19                               (b"chr2",1000,2000), # only peaks1 has chr2
  20                               (b"chr4",500,800),   # chr4 only one region, and not overlapping with peaks2
  21                             ]
  22         self.test_peaks2 = [  (b"chrY",100,200),
  23                               (b"chrY",300,400),
  24                               (b"chrY",600,800),
  25                               (b"chrY",1100,1300),
  26                               (b"chrY",1700,1800),
  27                               (b"chrX",1100,1200),
  28                               (b"chrX",1300,1400),
  29                               (b"chr1",2000,3000),
  30                               (b"chr3",1000, 5000), # only peaks2 has chr3
  31                               (b"chr4",1000,2000),
  32                             ]
  33         self.result_exclude2from1 = [ (b"chrY",0,100),
  34                                       (b"chrX",3000,4000),
  35                                       (b"chr2",1000,2000),
  36                                       (b"chr4",500,800),
  37                                      ]
  38         self.exclude2from1 = PeakIO()
  39         for a in self.result_exclude2from1:
  40             self.exclude2from1.add(a[0],a[1],a[2])
  41
  42     def test_exclude(self):
  43         r1 = PeakIO()
  44         for a in self.test_peaks1:
  45             r1.add(a[0],a[1],a[2])
  46         r2 = PeakIO()
  47         for a in self.test_peaks2:
  48             r2.add(a[0],a[1],a[2])
  49         r1.exclude(r2)
  50         result = str(r1)
  51         expected = str(self.exclude2from1)
  52         print( "result:\n",result )
  53         print( "expected:\n", expected )
  54         self.assertEqual( result, expected )
  55