/usr/lib/python3/dist-packages/pyBigWigTest/test.py is in python3-pybigwig 0.3.2-1.
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import tempfile
import os
import sys
import hashlib
class TestRemote():
fname = "http://raw.githubusercontent.com/dpryan79/pyBigWig/master/pyBigWigTest/test.bw"
def doOpen(self):
bw = pyBigWig.open(self.fname)
assert(bw is not None)
return bw
def doChroms(self, bw):
assert(bw.chroms() == {'1': 195471971, '10': 130694993})
assert(bw.chroms("1") == 195471971)
assert(bw.chroms("c") is None)
def doHeader(self, bw):
assert(bw.header() == {'maxVal': 2, 'sumData': 272, 'minVal': 0, 'version': 4, 'sumSquared': 500, 'nLevels': 1, 'nBasesCovered': 154})
def doStats(self, bw):
assert(bw.stats("1", 0, 3) == [0.2000000054637591])
assert(bw.stats("1", 0, 3, type="max") == [0.30000001192092896])
assert(bw.stats("1",99,200, type="max", nBins=2) == [1.399999976158142, 1.5])
assert(bw.stats("1") == [1.3351851569281683])
def doValues(self, bw):
assert(bw.values("1", 0, 3) == [0.10000000149011612, 0.20000000298023224, 0.30000001192092896])
#assert(bw.values("1", 0, 4) == [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, 'nan'])
def doIntervals(self, bw):
assert(bw.intervals("1", 0, 3) == ((0, 1, 0.10000000149011612), (1, 2, 0.20000000298023224), (2, 3, 0.30000001192092896)))
assert(bw.intervals("1") == ((0, 1, 0.10000000149011612), (1, 2, 0.20000000298023224), (2, 3, 0.30000001192092896), (100, 150, 1.399999976158142), (150, 151, 1.5)))
def doWrite(self, bw):
ofile = tempfile.NamedTemporaryFile(delete=False)
oname = ofile.name
ofile.close()
bw2 = pyBigWig.open(oname, "w")
assert(bw2 is not None)
#Since this is an unordered dict(), iterating over the items can swap the order!
chroms = [("1", bw.chroms("1")), ("10", bw.chroms("10"))]
assert(len(bw.chroms()) == 2)
bw2.addHeader(chroms, maxZooms=1)
#Copy the input file
for c in chroms:
ints = bw.intervals(c[0])
chroms2 = []
starts = []
ends = []
values = []
for entry in ints:
chroms2.append(c[0])
starts.append(entry[0])
ends.append(entry[1])
values.append(entry[2])
bw2.addEntries(chroms2, starts, ends=ends, values=values)
bw2.close()
#Ensure that the copied file has the same entries and max/min/etc.
bw2 = pyBigWig.open(oname)
assert(bw.header() == bw2.header())
assert(bw.chroms() == bw2.chroms())
for c in chroms:
ints1 = bw.intervals(c[0])
ints2 = bw2.intervals(c[0])
assert(ints1 == ints2)
bw.close()
bw2.close()
#Clean up
os.remove(oname)
def doWrite2(self):
'''
Test all three modes of storing entries. Also test to ensure that we get error messages when doing something silly
This is a modified version of the writing example from libBigWig
'''
chroms = ["1"]*6
starts = [0, 100, 125, 200, 220, 230, 500, 600, 625, 700, 800, 850]
ends = [5, 120, 126, 205, 226, 231]
values = [0.0, 1.0, 200.0, -2.0, 150.0, 25.0, 0.0, 1.0, 200.0, -2.0, 150.0, 25.0, -5.0, -20.0, 25.0, -5.0, -20.0, 25.0]
ofile = tempfile.NamedTemporaryFile(delete=False)
oname = ofile.name
ofile.close()
bw = pyBigWig.open(oname, "w")
bw.addHeader([("1", 1000000), ("2", 1500000)])
#Intervals
bw.addEntries(chroms[0:3], starts[0:3], ends=ends[0:3], values=values[0:3])
bw.addEntries(chroms[3:6], starts[3:6], ends=ends[3:6], values=values[3:6])
#IntervalSpans
bw.addEntries("1", starts[6:9], values=values[6:9], span=20)
bw.addEntries("1", starts[9:12], values=values[9:12], span=20)
#IntervalSpanSteps, this should instead take an int
bw.addEntries("1", 900, values=values[12:15], span=20, step=30)
bw.addEntries("1", 990, values=values[15:18], span=20, step=30)
#Attempt to add incorrect values. These MUST raise an exception
try:
bw.addEntries(chroms[0:3], starts[0:3], ends=ends[0:3], values=values[0:3])
assert(1==0)
except RuntimeError:
pass
try:
bw.addEntries("1", starts[6:9], values=values[6:9], span=20)
assert(1==0)
except RuntimeError:
pass
try:
bw.addEntries("3", starts[6:9], values=values[6:9], span=20)
assert(1==0)
except RuntimeError:
pass
try:
bw.addEntries("1", 900, values=values[12:15], span=20, step=30)
assert(1==0)
except RuntimeError:
pass
#Add a few intervals on a new chromosome
bw.addEntries(["2"]*3, starts[0:3], ends=ends[0:3], values=values[0:3])
bw.close()
#check md5sum, this is the simplest method to check correctness
h = hashlib.md5(open(oname, "rb").read()).hexdigest()
assert(h=="b1ca91d2ff42afdd2efa19a007c1ded4")
#Clean up
os.remove(oname)
def testAll(self):
bw = self.doOpen()
self.doChroms(bw)
self.doHeader(bw)
self.doStats(bw)
self.doValues(bw)
self.doIntervals(bw)
self.doWrite(bw)
if self.fname == "pyBigWigTest/test.bw":
self.doWrite2()
bw.close()
class TestLocal():
def testFoo(self):
blah = TestRemote()
blah.fname = os.path.dirname(pyBigWig.__file__) + "/pyBigWigTest/test.bw"
blah.testAll()
class TestBigBed():
def testBigBed(self):
fname = "http://www.encodeproject.org/files/ENCFF001JBR/@@download/ENCFF001JBR.bigBed"
bb = pyBigWig.open(fname)
assert(bb is not None)
assert(bb.isBigWig() == 0)
assert(bb.isBigBed() == 1)
SQL = """table RnaElements
"BED6 + 3 scores for RNA Elements data "
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Name of item"
uint score; "Normalized score from 0-1000"
char[1] strand; "+ or - or . for unknown"
float level; "Expression level such as RPKM or FPKM. Set to -1 for no data."
float signif; "Statistical significance such as IDR. Set to -1 for no data."
uint score2; "Additional measurement/count e.g. number of reads. Set to 0 for no data."
)
"""
output = bb.SQL()
if isinstance(output, bytes):
output = output.decode('ASCII')
assert(output == SQL)
o = bb.entries('chr1',10000000,10020000)
expected = [(10009333, 10009640, '61035\t130\t-\t0.026\t0.42\t404'), (10014007, 10014289, '61047\t136\t-\t0.029\t0.42\t404'), (10014373, 10024307, '61048\t630\t-\t5.420\t0.00\t2672399')]
assert(o == expected)
bb.close()
class TestNumpy():
def testNumpy(self):
import os
if pyBigWig.numpy == 0:
return 0
import numpy as np
bw = pyBigWig.open("/tmp/delete.bw", "w")
bw.addHeader([("1", 1000)], maxZooms=0)
# Type 0
chroms = np.array(["1"] * 10)
starts = np.array([0, 10, 20, 30, 40, 50, 60, 70, 80, 90], dtype=np.int64)
ends = np.array([5, 15, 25, 35, 45, 55, 65, 75, 85, 95], dtype=np.int64)
values0 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(chroms, starts, ends=ends, values=values0)
starts = np.array([100, 110, 120, 130, 140, 150, 160, 170, 180, 190], dtype=np.int64)
ends = np.array([105, 115, 125, 135, 145, 155, 165, 175, 185, 195], dtype=np.int64)
values1 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(chroms, starts, ends=ends, values=values1)
# Type 1, single chrom, multiple starts/values, single span
starts = np.array([200, 210, 220, 230, 240, 250, 260, 270, 280, 290], dtype=np.int64)
values2 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(np.str("1"), starts, span=np.int(8), values=values2)
starts = np.array([300, 310, 320, 330, 340, 350, 360, 370, 380, 390], dtype=np.int64)
values3 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(np.str("1"), starts, span=np.int(8), values=values3)
# Type 2, single chrom/start/span/step, multiple values
values4 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(np.str("1"), np.int(400), span=np.int(8), step=np.int64(2), values=values4)
values5 = np.array(np.random.random_sample(10), dtype=np.float64)
bw.addEntries(np.str("1"), np.int(500), span=np.int(8), step=np.int64(2), values=values5)
bw.close()
bw = pyBigWig.open("/tmp/delete.bw")
assert(bw is not None)
def compy(start, v2):
v = []
for t in bw.intervals("1", start, start + 100):
v.append(t[2])
v = np.array(v)
assert(np.all(np.abs(v - v2) < 1e-5))
compy(0, values0)
compy(100, values1)
compy(200, values2)
compy(300, values3)
compy(400, values4)
compy(500, values5)
# Get values as a numpy array
foo = bw.values("1", 0, 100, numpy=False)
assert(isinstance(foo, list))
foo = bw.values("1", 0, 100, numpy=True)
assert(isinstance(foo, np.ndarray))
bw.close()
os.remove("/tmp/delete.bw")
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