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from __future__ import print_function
import nose.tools
import numpy
import numpy.testing
import pbcore.data
from pbcore.data import MOVIE_NAME_BC
from pbcore.io.BarcodeH5Reader import BarcodeH5Reader, BarcodeH5Fofn, MPBarcodeH5Reader, LabeledZmw
class TestBarcodeH5Reader(object):
"""Tests of BarcodeH5Reader against a generic BarcodeH5 file
"""
def __init__(self):
bcFiles = pbcore.data.getBcH5s()
print(bcFiles)
self.bc1, self.bc2, self.bc3 = map(BarcodeH5Reader, bcFiles)
def test_BarcodeH5Reader_basicTest(self):
"""Test that BcH5Reader correctly sets movie name, barcode labels, and hole numbers
"""
nose.tools.assert_equal(MOVIE_NAME_BC, self.bc1.movieName)
numpy.testing.assert_array_equal(["F3--R3", "F4--R4", "F6--R6", "F7--R7"],
self.bc1.barcodeLabels)
numpy.testing.assert_array_equal([ 922, 1416, 1436, 1466, 1480, 1551,
1561, 1564, 1765, 1902, 1925, 1982,
2111, 2133, 2136, 2139, 2210, 2306],
self.bc1.holeNumbers)
nose.tools.assert_equal(MOVIE_NAME_BC, self.bc2.movieName)
numpy.testing.assert_array_equal(["F3--R3", "F4--R4", "F6--R6", "F7--R7"],
self.bc2.barcodeLabels)
numpy.testing.assert_array_equal([54505, 54506, 54507, 54516, 54535, 54542,
54543, 54547, 54562, 54588, 54618, 54622,
54632, 54633, 54645, 54650, 54653, 54658],
self.bc2.holeNumbers)
nose.tools.assert_equal(MOVIE_NAME_BC, self.bc3.movieName)
numpy.testing.assert_array_equal(["F3--R3", "F4--R4", "F6--R6", "F7--R7"],
self.bc3.barcodeLabels)
numpy.testing.assert_array_equal([108990, 109015, 109016, 109017, 109021, 109023,
109029, 109031, 109032, 109033, 109036, 109040,
109042, 109045, 109047, 109071, 109075, 109081],
self.bc3.holeNumbers)
def test_BarcodeH5Reader_iterator(self):
"""Test that BcH5Reader correctly iterates over it's labeled ZMWs
"""
labeledZmws1 = [ lZmw for lZmw in self.bc1.labeledZmws.values() ]
sortedZmws1 = sorted(labeledZmws1, key=lambda z: z.holeNumber)
nose.tools.assert_equal(sortedZmws1, list(self.bc1))
labeledZmws2 = [ lZmw for lZmw in self.bc2.labeledZmws.values() ]
sortedZmws2 = sorted(labeledZmws2, key=lambda z: z.holeNumber)
nose.tools.assert_equal(sortedZmws2, list(self.bc2))
labeledZmws3 = [ lZmw for lZmw in self.bc3.labeledZmws.values() ]
sortedZmws3 = sorted(labeledZmws3, key=lambda z: z.holeNumber)
nose.tools.assert_equal(sortedZmws3, list(self.bc3))
class TestBarcodeH5Fofn(object):
"""Tests of BarcodeH5RFofn against a generic 3 generic BarcodeH5 file
"""
def __init__(self):
bcFofn = pbcore.data.getBcFofn()
print(bcFofn)
self.bcFofn = BarcodeH5Fofn(bcFofn)
print(self.bcFofn)
def test_BasH5Fofn_basicTest(self):
"""Test that BcH5Fofn correctly sets movie name, barcode labels, and hole numbers
"""
nose.tools.assert_equal(1, len(self.bcFofn.movieNames))
numpy.testing.assert_array_equal(MOVIE_NAME_BC, self.bcFofn.movieNames[0])
numpy.testing.assert_array_equal(["F3--R3", "F4--R4", "F6--R6", "F7--R7"],
self.bcFofn.barcodeLabels)
nose.tools.assert_equal("paired", self.bcFofn.scoreMode)
numpy.testing.assert_array_equal([ 922, 1416, 1436, 1466, 1480, 1551,
1561, 1564, 1765, 1902, 1925, 1982,
2111, 2133, 2136, 2139, 2210, 2306,
54505, 54506, 54507, 54516, 54535, 54542,
54543, 54547, 54562, 54588, 54618, 54622,
54632, 54633, 54645, 54650, 54653, 54658,
108990, 109015, 109016, 109017, 109021, 109023,
109029, 109031, 109032, 109033, 109036, 109040,
109042, 109045, 109047, 109071, 109075, 109081],
self.bcFofn.holeNumbers)
def test_BcH5Fofn_iterator(self):
"""Test that BcH5Fofn correctly iterates over it's labeled ZMWs
"""
labeledZmws = [ lZmw for reader in self.bcFofn._bcH5s
for lZmw in reader ]
nose.tools.assert_equal(labeledZmws, list(self.bcFofn))
def test_BcH5Fofn_indexing(self):
"""Test that BcH5Fofn's indexing correctly slices and returns its contents
"""
holeNumTest = self.bcFofn[922]
nose.tools.assert_true(isinstance(holeNumTest, LabeledZmw))
nose.tools.assert_equal(holeNumTest.holeNumber, 922)
barcodeTest = self.bcFofn["F3--R3"]
nose.tools.assert_true(isinstance(barcodeTest, list))
barcodeTestHoleNums = [lzmw.holeNumber for lzmw in barcodeTest]
numpy.testing.assert_array_equal([ 1416, 1551, 1561, 1765, 1902, 1925, 2133,
54506, 54588, 54618, 109033, 109036, 109071, 109081],
barcodeTestHoleNums)
movieTest = self.bcFofn[MOVIE_NAME_BC]
nose.tools.assert_true(isinstance(movieTest, MPBarcodeH5Reader))
movieTestHoleNums = [lzmw.holeNumber for lzmw in movieTest]
numpy.testing.assert_array_equal([ 922, 1416, 1436, 1466, 1480, 1551,
1561, 1564, 1765, 1902, 1925, 1982,
2111, 2133, 2136, 2139, 2210, 2306,
54505, 54506, 54507, 54516, 54535, 54542,
54543, 54547, 54562, 54588, 54618, 54622,
54632, 54633, 54645, 54650, 54653, 54658,
108990, 109015, 109016, 109017, 109021, 109023,
109029, 109031, 109032, 109033, 109036, 109040,
109042, 109045, 109047, 109071, 109075, 109081],
movieTestHoleNums)
movieBarcodeTest = self.bcFofn[MOVIE_NAME_BC + "/F3--R3"]
movieBarcodeTestHoleNums = [lzmw.holeNumber for lzmw in movieBarcodeTest]
numpy.testing.assert_array_equal([ 1416, 1551, 1561, 1765, 1902, 1925, 2133,
54506, 54588, 54618, 109033, 109036, 109071, 109081],
movieBarcodeTestHoleNums)
zmwTest = self.bcFofn[MOVIE_NAME_BC + "/922"]
nose.tools.assert_equal(zmwTest.holeNumber, 922)
subreadTest = self.bcFofn[MOVIE_NAME_BC + "/922/0_1000"]
nose.tools.assert_equal(subreadTest.holeNumber, 922)
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