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#!/usr/bin/env python
# Time-stamp: <2024-05-15 19:31:36 Tao Liu>
import pytest
from MACS3.Signal.BedGraph import *
from MACS3.IO.PeakIO import PeakIO
test_regions1 = [(b"chrY",0,10593155,0.0),
(b"chrY",10593155,10597655,0.0066254580149)]
overlie_max = [(b"chrY", 0, 75, 20.0), # max
(b"chrY", 75, 85, 35.0),
(b"chrY", 85, 90, 75.0),
(b"chrY", 90,150, 10.0),
(b"chrY",150,155, 0.0)]
overlie_mean = [(b"chrY", 0, 70, 6.66667), # mean
(b"chrY", 70, 75, 9),
(b"chrY", 75, 80, 14),
(b"chrY", 80, 85, 11.66667),
(b"chrY", 85, 90, 36.66667),
(b"chrY", 90,150, 3.33333),
(b"chrY",150,155, 0.0)]
overlie_fisher = [(b"chrY", 0, 70, (0,0,20), 92.10340371976183, 1.1074313239555578e-17, 16.9557 ), # fisher
(b"chrY", 70, 75, (7,0,20), 124.33959502167846, 1.9957116587802055e-24, 23.6999 ),
(b"chrY", 75, 80, (7,0,35), 193.41714781149986, 4.773982707347631e-39, 38.3211 ),
(b"chrY", 80, 85, (0,0,35), 161.1809565095832, 3.329003070922764e-32, 31.4777),
(b"chrY", 85, 90, (0,75,35), 506.56872045869005, 3.233076792862357e-106, 105.4904),
(b"chrY", 90,150, (0,0,10), 46.051701859880914, 2.8912075645386016e-08, 7.5389),
(b"chrY",150,155, (0,0,0), 0, 1.0, 0.0)]
some_peak = [(b"chrY", 50, 80),
(b"chrY", 95, 152)]
@pytest.fixture
def define_regions():
test_regions1 = [(b"chrY",0,70,0.00),
(b"chrY",70,80,7.00),
(b"chrY",80,150,0.00)]
test_regions2 = [(b"chrY",0,85,0.00),
(b"chrY",85,90,75.00),
(b"chrY",90,155,0.00)]
test_regions3 = [(b"chrY",0,75,20.0),
(b"chrY",75,90,35.0),
(b"chrY",90,150,10.0)]
bdg1 = bedGraphTrackI()
bdg2 = bedGraphTrackI()
bdg3 = bedGraphTrackI()
for a in test_regions1:
bdg1.add_loc(a[0],a[1],a[2],a[3])
for a in test_regions2:
bdg2.add_loc(a[0],a[1],a[2],a[3])
for a in test_regions3:
bdg3.add_loc(a[0],a[1],a[2],a[3])
return (bdg1, bdg2, bdg3)
def test_add_loc1( ):
bdg = bedGraphTrackI()
for a in test_regions1:
bdg.add_loc(a[0],a[1],a[2],a[3])
def test_overlie_max( define_regions ):
(bdg1,bdg2,bdg3) = define_regions
bdgb = bdg1.overlie([bdg2,bdg3], func="max")
chrom = b"chrY"
(p,v) = bdgb.get_data_by_chr(chrom)
pre = 0
for i in range(len(p)):
pos = p[i]
value = v[i]
assert pre == pytest.approx( overlie_max[i][1] )
assert pos == pytest.approx( overlie_max[i][2] )
assert value == pytest.approx( overlie_max[i][3] )
pre = pos
def test_refine_peak():
bdg = bedGraphTrackI()
for a in overlie_mean:
bdg.add_loc(a[0], a[1], a[2], a[3])
peak = PeakIO()
for a in some_peak:
peak.add( a[0], a[1], a[2])
new_peak = bdg.refine_peaks( peak )
out = str(new_peak)
std = "chrom:chrY\tstart:50\tend:80\tname:peak_1\tscore:14\tsummit:77\nchrom:chrY\tstart:95\tend:152\tname:peak_2\tscore:3.33333\tsummit:122\n"
assert out == std
# def test_overlie_mean(self):
# bdgb = self.bdg1.overlie([self.bdg2,self.bdg3], func="mean")
# chrom = b"chrY"
# (p,v) = bdgb.get_data_by_chr(chrom)
# pre = 0
# for i in range(len(p)):
# pos = p[i]
# value = v[i]
# self.assertEqual_float( self.test_overlie_mean[i][1], pre )
# self.assertEqual_float( self.test_overlie_mean[i][2], pos )
# self.assertEqual_float( self.test_overlie_mean[i][3], value )
# pre = pos
# def test_overlie_fisher(self):
# bdgb = self.bdg1.overlie([self.bdg2,self.bdg3], func="fisher")
# chrom = b"chrY"
# (p,v) = bdgb.get_data_by_chr(chrom)
# pre = 0
# for i in range(len(p)):
# pos = p[i]
# value = v[i]
# self.assertEqual_float( self.test_overlie_fisher[i][1], pre )
# self.assertEqual_float( self.test_overlie_fisher[i][2], pos )
# self.assertEqual_float( self.test_overlie_fisher[i][6], value )
# pre = pos
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