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# from unittest import TestCase
import deeptools.countReadsPerBin as cr
import numpy as np
import numpy.testing as nt
import os.path
__author__ = 'Fidel'
ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
class TestCountReadsPerBin(object):
def setUp(self):
"""
The distribution of reads between the two bam files is as follows.
They cover 200 bp::
0 100 200
|------------------------------------------------------------|
A ==============>
<==============
B <============== ==============>
==============>
==============>
"""
self.root = ROOT
self.bamFile1 = self.root + "testA.bam"
self.bamFile2 = self.root + "testB.bam"
self.bamFile_PE = self.root + "test_paired2.bam"
self.chrom = '3R'
step_size = 50
bin_length = 25
self.c = cr.CountReadsPerBin([self.bamFile1, self.bamFile2],
binLength=bin_length,
stepSize=step_size)
def test_count_reads_in_region(self):
self.c.skipZeros = False
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200)
nt.assert_equal(resp, np.array([[0, 0.],
[0, 1.],
[1, 1.],
[1, 2.]]))
def test_count_reads_in_region_extension_1(self):
"""
In this case when read extension is smaller than read length
extension is turned off and a warning is printed.
"""
self.c = cr.CountReadsPerBin([self.bamFile1, self.bamFile2],
binLength=1,
stepSize=50,
extendReads=25)
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200)
nt.assert_equal(resp, np.array([[0, 0.],
[0, 1.],
[1, 1.],
[1, 2.]]))
def test_count_reads_in_region_total(self):
""" count the reads over the whole region
2 for the first case, and 4 for the second
"""
self.c.skipZeros = False
self.c.stepSize = 200
self.c.binLength = 200
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200)
nt.assert_equal(resp, np.array([[2, 4.]]))
def test_countReadsInRegions_min_mapping_quality(self):
# Test min mapping quality.
self.c.minMappingQuality = 40
self.c.skipZeros = False
resp, _ = self.c.count_reads_in_region(self. chrom, 0, 200)
nt.assert_equal(resp, np.array([[0, 0, 0, 1.],
[0, 0, 0, 1.]]).T)
def test_count_reads_in_region_ignore_duplicates(self):
# Test ignore duplicates
self.c.skipZeros = False
self.c.ignoreDuplicates = True
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200)
nt.assert_equal(resp, np.array([[0, 0, 1, 1.],
[0, 1, 1, 1.]]).T)
def test_count_reads_in_region_ignore_bed_regions(self):
# Test bed regions:
bed_regions = [[self.chrom, [(10, 20)], "."], [self.chrom, [(150, 160)], "."]]
self.c.skipZeros = False
self.c.binLength = 10
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200, bed_regions_list=bed_regions)
nt.assert_equal(resp, np.array([[0, 1.],
[0, 2.]]).T)
def test_get_coverage_of_region_sam_flag_include(self):
self.c.samFlag_include = 16 # include reverse reads only
self.c.bamFilesList = [self.bamFile1]
resp, _ = self.c.count_reads_in_region('3R', 0, 200)
nt.assert_array_equal(resp, np.array([[0], [0], [0], [1]]))
def test_get_coverage_of_region_sam_flag_exclude(self):
self.c.samFlag_exclude = 16 # exclude reverse reads
self.c.bamFilesList = [self.bamFile1]
resp, _ = self.c.count_reads_in_region('3R', 0, 200)
nt.assert_array_equal(resp, np.array([[0], [0], [1], [0]]))
def test_get_coverage_of_region_large_bin(self):
self.c.bamFilesList = [self.bamFile2]
self.c.binLength = 200
self.c.stepSize = 200
resp, _ = self.c.count_reads_in_region('3R', 0, 200)
nt.assert_array_equal(resp, np.array([[4]]))
def test_get_coverage_of_region_ignore_duplicates(self):
self.c.ignoreDuplicates = True
self.c.bamFilesList = [self.bamFile2]
resp, _ = self.c.count_reads_in_region('3R', 0, 200)
nt.assert_array_equal(resp, np.array([[0.],
[1.],
[1.],
[1.]]))
# check zero to nans
self.c.zerosToNans = True
resp, _ = self.c.count_reads_in_region('3R', 0, 200)
nt.assert_array_equal(resp, np.array([[np.nan],
[1.],
[1.],
[1.]]))
def test_get_coverage_of_region_split_read(self):
"""
The bamFile1 contains a read at position 10
with the following CIGAR: 10S20M10N10M10S
that maps to a chromosome named chr_cigar.
"""
# turn of read extension
self.c.extendPairedEnds = False
self.c.bamFilesList = [self.bamFile1]
self.c.binLength = 10
self.c.stepSize = 10
resp, _ = self.c.count_reads_in_region('chr_cigar', 0, 100)
nt.assert_array_equal(resp, np.array([[0.],
[1.],
[1.],
[0.],
[1.],
[0.],
[0.],
[0.],
[0.],
[0.]]))
def test_get_coverage_of_region_zeros_to_nan(self):
self.c.zerosToNans = True
resp, _ = self.c.count_reads_in_region(self.chrom, 0, 200)
nt.assert_equal(resp, np.array([[np.nan, np.nan],
[np.nan, 1],
[1, 1],
[1, 2]]))
def test_bed_file(self):
bed = "chr3R\t0\t10\nchr3R\t110\t120\nchr3R\t160\t180"
import tempfile
bed_file = tempfile.NamedTemporaryFile(suffix=".bed", delete=False, mode="w")
bed_file.write(bed)
bed_file.close()
self.c = cr.CountReadsPerBin([self.bamFile2],
bedFile=[bed_file.name])
resp = self.c.run()
nt.assert_equal(resp, np.array([[0.],
[1.],
[2.]]))
import os
os.unlink(bed_file.name)
class TestCountReadsPerBinCRAM(TestCountReadsPerBin):
def setUp(self):
"""
As above, but using CRAM rather than BAM
The distribution of reads between the two bam files is as follows.
They cover 200 bp::
0 100 200
|------------------------------------------------------------|
A ==============>
<==============
B <============== ==============>
==============>
==============>
"""
self.root = ROOT
self.bamFile1 = self.root + "testA.cram"
self.bamFile2 = self.root + "testB.cram"
self.bamFile_PE = self.root + "test_paired2.cram"
self.chrom = '3R'
step_size = 50
bin_length = 25
self.c = cr.CountReadsPerBin([self.bamFile1, self.bamFile2],
binLength=bin_length,
stepSize=step_size)
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