test/test_Pileup.py

   1 #!/usr/bin/env python
   2 # Time-stamp: <2019-09-20 15:06:44 taoliu>
   3
   4 """Module Description: Test functions for pileup functions.
   5
   6 This code is free software; you can redistribute it and/or modify it
   7 under the terms of the BSD License (see the file LICENSE included with
   8 the distribution).
   9 """
  10
  11 import unittest
  12
  13 from math import log10
  14 from MACS2.Pileup import *
  15 from MACS2.IO.FixWidthTrack import FWTrack
  16
  17 # ------------------------------------
  18 # Main function
  19 # ------------------------------------
  20
  21 class Test_pileup(unittest.TestCase):
  22     """Unittest for pileup_bdg() in Pileup.pyx.
  23
  24     """
  25     def setUp(self):
  26         self.maxDiff = None
  27         self.chrom = b"chr1"
  28         self.plus_pos = ( 0, 1, 3, 4, 5 )
  29         self.minus_pos = ( 5, 6, 8, 9, 10 )
  30         self.d = 5
  31         self.scale_factor = 0.5
  32         self.expect = [ ( 0, 1, 1.0 ),
  33                         ( 1, 3, 2.0 ),
  34                         ( 3, 4, 3.0 ),
  35                         ( 4, 6, 4.0 ),
  36                         ( 6, 8, 3.0 ),
  37                         ( 8, 9, 2.0 ),
  38                         ( 9, 10, 1.0 )
  39                         ]
  40         self.expect2 = [(0, 1, 13.0),
  41                         (1, 3, 14.0),
  42                         (3, 4, 16.0),
  43                         (4, 6, 18.0),
  44                         (6, 8, 16.0),
  45                         (8, 9, 14.0),
  46                         (9, 10, 13.0)]
  47
  48         self.d_s = [ 5, 10, 100 ]
  49         self.scale_factor_s = [ 0.5, 1, 2 ]
  50
  51     def test_pileup(self):
  52         # build FWTrackII
  53         self.fwtrack2 = FWTrack()
  54         for i in self.plus_pos:
  55             self.fwtrack2.add_loc(self.chrom, i, 0)
  56         for i in self.minus_pos:
  57             self.fwtrack2.add_loc(self.chrom, i, 1)
  58         self.fwtrack2.finalize()
  59
  60         self.pileup = unified_pileup_bdg(self.fwtrack2, self.d, self.scale_factor, halfextension=False)
  61         self.result = []
  62         chrs = self.pileup.get_chr_names()
  63         for chrom in chrs:
  64             (p,v) = self.pileup.get_data_by_chr(chrom)
  65             pnext = iter(p).__next__
  66             vnext = iter(v).__next__
  67             pre = 0
  68             for i in range(len(p)):
  69                 pos = pnext()
  70                 value = vnext()
  71                 self.result.append( (pre,pos,value) )
  72                 pre = pos
  73         # check result
  74         self.assertEqual(self.result, self.expect)
  75
  76     def test_pileup_w_multiple_d_bdg ( self ):
  77         # build FWTrackII
  78         self.fwtrack2 = FWTrack(fw=5)
  79         for i in self.plus_pos:
  80             self.fwtrack2.add_loc(self.chrom, i, 0)
  81         for i in self.minus_pos:
  82             self.fwtrack2.add_loc(self.chrom, i, 1)
  83         self.fwtrack2.finalize()
  84         # pileup test
  85         self.pileup = unified_pileup_bdg(self.fwtrack2, self.d_s, self.scale_factor_s, baseline_value=13, halfextension=False)
  86         self.result = []
  87         chrs = self.pileup.get_chr_names()
  88         for chrom in chrs:
  89             (p,v) = self.pileup.get_data_by_chr(chrom)
  90             pnext = iter(p).__next__
  91             vnext = iter(v).__next__
  92             pre = 0
  93             for i in range(len(p)):
  94                 pos = pnext()
  95                 value = vnext()
  96                 self.result.append( (pre,pos,value) )
  97                 pre = pos
  98         # check result
  99         self.assertEqual(self.result, self.expect2)
 100