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import os
import sys
import deeptools.computeMatrix
import deeptools.plotHeatmap
import deeptools.plotProfile
import deeptools.utilities
import json
__author__ = 'Fidel'
ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_heatmapper/"
def cmpMatrices(f1, f2):
"""
The header produced by computeMatrix will be different every time a command is run in python3!
"""
rv = True
file1 = open(f1)
file2 = open(f2)
for l1, l2 in zip(file1, file2):
if isinstance(l1, bytes):
l1 = l1.decode()
l2 = l2.decode()
l1 = l1.strip()
l2 = l2.strip()
if l1.startswith("@"):
p1 = json.loads(l1[1:])
p2 = json.loads(l2[1:])
for k, v in p1.items():
if k not in p2.keys():
sys.stderr.write("key in {} missing: {} not in {}\n".format(f1, k, p2.keys()))
rv = False
if p1[k] != p2[k]:
sys.stderr.write("values of '{}' is different: {} not in {}\n".format(k, p1[k], p2[k]))
rv = False
for k in p2.keys():
if k not in p1.keys():
sys.stderr.write("key in {} missing: {} not in {}\n".format(f2, k, p1.keys()))
rv = False
else:
if l1 != l2:
sys.stderr.write("lines differ:\n{}\n vs\n{}\n".format(l1, l2))
rv = False
file1.close()
file2.close()
return rv
def test_computeMatrix_reference_point():
args = "reference-point -R {0}/test2.bed -S {0}/test.bw -b 100 -a 100 " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_reference_point_center():
args = "reference-point -R {0}/test2.bed -S {0}/test.bw -b 100 -a 100 --referencePoint center " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_center.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_reference_point_tes():
args = "reference-point -R {0}/test2.bed -S {0}/test.bw -b 100 -a 100 --referencePoint TES " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_TES.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_reference_point_missing_data_as_zero():
args = "reference-point -R {0}/test2.bed -S {0}/test.bw -b 100 -a 100 " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1 --missingDataAsZero".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_nan_to_zero.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_scale_regions():
args = "scale-regions -R {0}/test2.bed -S {0}/test.bw -b 100 -a 100 -m 100 " \
"--outFileName /tmp/_test2.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test2.mat.gz')
assert cmpMatrices(ROOT + '/master_scale_reg.mat', '/tmp/_test2.mat') is True
os.remove('/tmp/_test2.mat')
def test_computeMatrix_multiple_bed():
args = "reference-point -R {0}/group1.bed {0}/group2.bed -S {0}/test.bw -b 100 -a 100 " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_multibed.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_region_extend_over_chr_end():
args = "reference-point -R {0}/group1.bed {0}/group2.bed -S {0}/test.bw -b 100 -a 500 " \
"--outFileName /tmp/_test.mat.gz -bs 1 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_extend_beyond_chr_size.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_unscaled():
args = "scale-regions -S {0}/unscaled.bigWig -R {0}/unscaled.bed -a 300 -b 500 --unscaled5prime 100 --unscaled3prime 50 " \
"--outFileName /tmp/_test.mat.gz -bs 10 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test.mat.gz')
assert cmpMatrices(ROOT + '/master_unscaled.mat', '/tmp/_test.mat') is True
os.remove('/tmp/_test.mat')
def test_computeMatrix_gtf():
args = "scale-regions -S {0}../test_data/test1.bw.bw -R {0}../test_data/test.gtf -a 300 -b 500 --unscaled5prime 20 --unscaled3prime 50 " \
"--outFileName /tmp/_test_gtf.mat.gz -bs 10 -p 1".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test_gtf.mat.gz')
assert cmpMatrices(ROOT + '/master_gtf.mat', '/tmp/_test_gtf.mat') is True
os.remove('/tmp/_test_gtf.mat')
def test_computeMatrix_metagene():
args = "scale-regions -S {0}../test_data/test1.bw.bw -R {0}../test_data/test.gtf -a 300 -b 500 --unscaled5prime 20 --unscaled3prime 50 " \
"--outFileName /tmp/_test_metagene.mat.gz -bs 10 -p 1 --metagene".format(ROOT).split()
deeptools.computeMatrix.main(args)
os.system('gunzip -f /tmp/_test_metagene.mat.gz')
assert cmpMatrices(ROOT + '/master_metagene.mat', '/tmp/_test_metagene.mat') is True
os.remove('/tmp/_test_metagene.mat')
def test_chopRegions_body():
region = [(0, 200), (300, 400), (800, 900)]
lbins, bodybins, rbins, padLeft, padRight = deeptools.heatmapper.chopRegions(region, left=0, right=0)
assert(lbins == [])
assert(rbins == [])
assert(bodybins == region)
assert(padLeft == 0)
assert(padRight == 0)
# Unscaled 5', 3'
lbins, bodybins, rbins, padLeft, padRight = deeptools.heatmapper.chopRegions(region, left=150, right=150)
assert(lbins == [(0, 150)])
assert(rbins == [(350, 400), (800, 900)])
assert(bodybins == [(150, 200), (300, 350)])
assert(padLeft == 0)
assert(padRight == 0)
def test_chopRegions_TSS():
region = [(0, 200), (300, 400), (800, 900)]
# + strand, 250 downstream
downstream, body, unscaled3prime, padRight, _ = deeptools.heatmapper.chopRegions(region, left=250)
assert(downstream == [(0, 200), (300, 350)])
assert(body == [(350, 400), (800, 900)])
assert(unscaled3prime == [])
assert(padRight == 0)
assert(_ == 0)
# + strand, 500 downstream
downstream, body, unscaled3prime, padRight, _ = deeptools.heatmapper.chopRegions(region, left=500)
assert(downstream == region)
assert(body == [])
assert(unscaled3prime == [])
assert(padRight == 100)
assert(_ == 0)
# - strand, 250 downstream (labeled "upstream" due to being on the - strand)
unscaled5prime, body, upstream, _, padLeft = deeptools.heatmapper.chopRegions(region, right=250)
assert(upstream == [(150, 200), (300, 400), (800, 900)])
assert(body == [(0, 150)])
assert(unscaled5prime == [])
assert(padLeft == 0)
assert(_ == 0)
# - strand, 500 downstream (labeled "upstream" due to being on the - strand)
unscaled5prime, body, upstream, _, padLeft = deeptools.heatmapper.chopRegions(region, right=500)
assert(upstream == region)
assert(body == [])
assert(unscaled5prime == [])
assert(padLeft == 100)
assert(_ == 0)
def test_chopRegions_TES():
region = [(0, 200), (300, 400), (800, 900)]
# + strand, 250 upstream
unscaled5prime, body, upstream, _, padLeft = deeptools.heatmapper.chopRegions(region, right=250)
assert(unscaled5prime == [])
assert(body == [(0, 150)])
assert(upstream == [(150, 200), (300, 400), (800, 900)])
assert(_ == 0)
assert(padLeft == 0)
# + strand, 500 upstream
unscaled5prime, body, upstream, _, padLeft = deeptools.heatmapper.chopRegions(region, right=500)
assert(unscaled5prime == [])
assert(body == [])
assert(upstream == region)
assert(_ == 0)
assert(padLeft == 100)
# + strand, 250 downstream (labeled "upstream" due to being on the - strand)
downstream, body, unscaled3prime, padRight, _ = deeptools.heatmapper.chopRegions(region, left=250)
assert(downstream == [(0, 200), (300, 350)])
assert(body == [(350, 400), (800, 900)])
assert(unscaled3prime == [])
assert(padRight == 0)
assert(_ == 0)
# + strand, 500 downstream (labeled "upstream" due to being on the - strand)
downstream, body, unscaled3prime, padRight, _ = deeptools.heatmapper.chopRegions(region, left=500)
assert(downstream == region)
assert(body == [])
assert(unscaled3prime == [])
assert(padRight == 100)
assert(_ == 0)
def test_chopRegionsFromMiddle():
region = [(0, 200), (300, 400), (800, 900)]
# + strand, 100 upstream/200 downstream
upstream, downstream, padLeft, padRight = deeptools.heatmapper.chopRegionsFromMiddle(region, left=100, right=200)
assert(upstream == [(100, 200)])
assert(downstream == [(300, 400), (800, 900)])
assert(padLeft == 0)
assert(padRight == 0)
# + strand, 250 upstream/300 downstream
upstream, downstream, padLeft, padRight = deeptools.heatmapper.chopRegionsFromMiddle(region, left=250, right=300)
assert(upstream == [(0, 200)])
assert(downstream == [(300, 400), (800, 900)])
assert(padLeft == 50)
assert(padRight == 100)
# - strand, 100 upstream/200 downstream
upstream, downstream, padLeft, padRight = deeptools.heatmapper.chopRegionsFromMiddle(region, left=200, right=100)
assert(upstream == [(0, 200)])
assert(downstream == [(300, 400)])
assert(padLeft == 0)
assert(padRight == 0)
# - strand, 250 upstream/300 downstream
upstream, downstream, padLeft, padRight = deeptools.heatmapper.chopRegionsFromMiddle(region, left=300, right=250)
assert(upstream == [(0, 200)])
assert(downstream == [(300, 400), (800, 900)])
assert(padLeft == 100)
assert(padRight == 50)
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