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|
import inspect
import os
import h5py
import nose.tools
import numpy
import numpy.testing
import pbcore.data
from pbcore.io.BasH5IO import BasH5Reader, Zmw, ZmwRead, CCSZmwRead
from pbcore.chemistry import ChemistryLookupError
class TestBasH5Reader_14(object):
"""Tests of BasH5Reader against a 1.4 bas.h5 file, no multipart with
CCS.
"""
def __init__(self):
self.cmpH5 = pbcore.io.CmpH5Reader(pbcore.data.getCmpH5())
basFiles = pbcore.data.getBasH5s()
self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
def test_BasH5Reader_basicTest(self):
"""Test that BasH5Reader correctly sets moviename, identifies the
sequencingZmws, and finds the subreads for each Zmw.
"""
nose.tools.assert_equal(pbcore.data.MOVIE_NAME_14, self.bas1.movieName)
numpy.testing.assert_array_equal([ 7, 8, 9, 1000, 1006, 1007,
2001, 2003, 2007, 2008, 3004, 3006,
3008, 4004, 4005, 4006, 4007, 4009],
self.bas1.sequencingZmws)
numpy.testing.assert_array_equal([ 7, 8, 9, 1000, 1001, 1002,
1003, 1004, 1005, 1006, 1007, 1008,
1009, 2000, 2001, 2002, 2003, 2004,
2005, 2006, 2007, 2008, 2009, 3000,
3001, 3002, 3003, 3004, 3005, 3006,
3007, 3008, 3009, 4000, 4001, 4002,
4003, 4004, 4005, 4006, 4007, 4008,
4009],
self.bas1.allSequencingZmws)
for zmw in self.bas1:
nose.tools.assert_greater(len(zmw.subreads), 0)
def test_BasH5Reader_basecallsVsCmpH5(self):
"""Compare datasets in the bas.h5 file against those in a corresponding
cmp.h5 file.
"""
aln = self.cmpH5[2]
nose.tools.assert_equal(os.path.join(pbcore.data.MOVIE_NAME_14, "2001", "3580_3922"),
aln.readName)
zmwRead = self.bas1[2001].read(3580, 3922)
nose.tools.assert_equal(os.path.join(pbcore.data.MOVIE_NAME_14, "2001", "3580_3922"),
zmwRead.readName)
# Verify that the bases and a couple of quality values are the same
nose.tools.assert_equal(aln.read(aligned=False), zmwRead.basecalls())
numpy.testing.assert_array_equal(aln.InsertionQV(aligned=False),
zmwRead.InsertionQV())
numpy.testing.assert_array_equal(aln.DeletionQV(aligned=False),
zmwRead.DeletionQV())
numpy.testing.assert_array_equal(aln.QualityValue(aligned=False),
zmwRead.QualityValue())
def test_BasH5Reader_regionTableAccessors(self):
"""Test that BasH5Reader can read the region table and find
HQ, insert, and adapter regions.
"""
zmw = self.bas1[7]
numpy.testing.assert_array_equal(
numpy.array([(7, 1, 0, 299, -1),
(7, 1, 343, 991, -1),
(7, 1, 1032, 1840, -1),
(7, 0, 299, 343, 681),
(7, 0, 991, 1032, 804),
(7, 2, 0, 1578, 0)],
dtype=(numpy.record, [('holeNumber', '<i4'),
('regionType', '<i4'),
('regionStart', '<i4'),
('regionEnd', '<i4'),
('regionScore', '<i4')])),
zmw.regionTable.view(dtype=numpy.ndarray))
nose.tools.assert_equal((0, 1578), zmw.hqRegion)
nose.tools.assert_equal([(299, 343), (991, 1032)], zmw.adapterRegions)
nose.tools.assert_equal([(0, 299), (343, 991), (1032, 1578)],
zmw.insertRegions)
def test_BasH5Reader_ccs(self):
"""Test that BasH5Reader can read the CCS bases."""
nose.tools.assert_equal(self.bas1[4006].ccsRead.basecalls(),
''.join(['GGCGCACGGAGGAGCAAGCGTGACAGTCCCACGTCATGCCCGCCGACG',
'ATATCGAGCTCGCGCTCACCGCCAGGGTGTGAAGTGAATTCACGGTGC',
'CGCCGAAAGCTGGGCCGGCTTTCGTTCCTTCGCCGGTCAGGAGAAGGC',
'GGACCCCGTCGTGGGCCATTCCGAGCCTGGAGACAGCGGTCGAAAAAG',
'CCTTCGCCAAGCCGGTGGCCAAATGGTCGGCCAGCGAGAATCCGTGC']))
def test_BasH5Reader_productivity(self):
nose.tools.assert_equal(1, self.bas1[4006].productivity)
def test_BasH5Reader_readScore(self):
nose.tools.assert_almost_equal(0.7822426, self.bas1[4006].readScore)
@nose.tools.raises(ChemistryLookupError)
def test_14_missing_chemistry(self):
"""Tests that we raise an exception when we can't find chemistry information"""
self.bas1.sequencingChemistry
def test_ZmwRead_len(self):
"""Test that ZmwRead objects have the correct len."""
nose.tools.assert_equal(1126, len(self.bas1[4006].read().basecalls()))
nose.tools.assert_equal(1126, len(self.bas1[4006].read()))
nose.tools.assert_equal(464,
len(self.bas1[4006].subreads[0].basecalls()))
nose.tools.assert_equal(464, len(self.bas1[4006].subreads[0]))
nose.tools.assert_equal(239, len(self.bas1[4006].ccsRead.basecalls()))
nose.tools.assert_equal(239, len(self.bas1[4006].ccsRead))
class CommonTests(object):
ZMW_ATTRIBUTES = ['QualityValue', 'InsertionQV', 'DeletionQV',
'DeletionTag', 'SubstitutionQV', 'SubstitutionTag',
'MergeQV', 'IPD', 'PreBaseFrames', 'PulseWidth',
'WidthInFrames']
def test_all_fields_accessible(self):
# Test that zmws have correct pulse/quality attributes
reader = pbcore.io.BasH5Reader(self.bash5_filename)
for zmw in reader.sequencingZmws:
read = reader[zmw].read()
for attribute in self.ZMW_ATTRIBUTES:
nose.tools.assert_is_instance(getattr(read, attribute)(),
numpy.ndarray)
numpy.testing.assert_array_equal(read.IPD(), read.PreBaseFrames())
numpy.testing.assert_array_equal(read.PulseWidth(),
read.WidthInFrames())
def test_zmw_region_table(self):
reader = pbcore.io.BasH5Reader(self.bash5_filename)
sequencing_zmws = set(reader.sequencingZmws)
for zmw in reader.allSequencingZmws:
region_table = reader[zmw].regionTable.tolist()
hq_entry = [k for k in region_table if k[1] == 2][0]
hq_size = hq_entry[3] - hq_entry[2]
# Sequencing Zmws should have an HQ region
if zmw not in sequencing_zmws:
nose.tools.assert_equal(hq_size, 0)
else:
nose.tools.assert_greater(hq_size, 0)
for entry in region_table:
nose.tools.assert_equal(entry[0], zmw)
nose.tools.assert_less_equal(entry[2], entry[3])
reader.close()
class ReadIteratorTests(object):
def test_read_iterators(self):
for fname in [self.bash5_filename] + self.baxh5_filenames:
reader = pbcore.io.BasH5Reader(self.bash5_filename)
if reader.hasConsensusBasecalls:
ccsReads = [ zmw.ccsRead
for zmw in reader
if zmw.ccsRead is not None ]
nose.tools.assert_equal(ccsReads, list(reader.ccsReads()))
else:
nose.tools.assert_equal([], list(reader.ccsReads()))
if reader.hasRawBasecalls:
subreads = [ subread
for zmw in reader
for subread in zmw.subreads ]
nose.tools.assert_equal(subreads, list(reader.subreads()))
reads = [ zmw.read()
for zmw in reader ]
nose.tools.assert_equal(reads, list(reader.reads()))
else:
nose.tools.assert_equal([], list(reader.reads()))
nose.tools.assert_equal([], list(reader.subreads()))
class CommonMultiPartTests(object):
def test_multipart_constructor_bash5(self):
# Test the constuctor of a multipart bas.h5 file
reader = pbcore.io.BasH5Reader(self.bash5_filename)
nose.tools.assert_is_instance(reader.file, h5py.File)
# Should have three parts for v2.0 and v2.1
nose.tools.assert_equal(len(reader.parts), 3)
nose.tools.assert_list_equal(self.baxh5_filenames,
[k.filename for k in reader.parts])
# All bas.h5 files should have raw base calls. 2.1 bas.h5 files don't
# have consensus base calls
nose.tools.assert_true(reader.hasRawBasecalls)
for zmw in reader.sequencingZmws:
nose.tools.assert_in(zmw, reader.allSequencingZmws)
nose.tools.assert_is_instance(reader[zmw], Zmw)
nose.tools.assert_less_equal(len(reader.sequencingZmws),
len(reader.allSequencingZmws))
reader.close()
def test_multippart_constructor_baxh5(self):
# Test constructor of baxh5 files
for filename in self.baxh5_filenames:
reader = pbcore.io.BasH5Reader(filename)
nose.tools.assert_is_instance(reader.file, h5py.File)
nose.tools.assert_equal(len(reader.parts), 1)
nose.tools.assert_true(reader.hasRawBasecalls)
for zmw in reader.sequencingZmws:
nose.tools.assert_in(zmw, reader.allSequencingZmws)
nose.tools.assert_is_instance(reader[zmw], Zmw)
nose.tools.assert_less_equal(len(reader.sequencingZmws),
len(reader.allSequencingZmws))
reader.close()
def test_multipart_hole_lookup(self):
# Test that multipart files look up files and hole numbers correctly
hole_number_to_filename = {}
for filename in self.baxh5_filenames:
f = h5py.File(filename, 'r')
for hole_number in f['PulseData/BaseCalls/ZMW/HoleNumber']:
hole_number_to_filename[hole_number] = filename
f.close()
reader = pbcore.io.BasH5Reader(self.bash5_filename)
for hole_number in hole_number_to_filename:
zmw = reader[hole_number]
nose.tools.assert_equal(zmw.baxH5.filename,
hole_number_to_filename[hole_number])
nose.tools.assert_is_instance(zmw, Zmw)
reader.close()
def _clip_region(self, region, hq_region):
end = min(region[1], hq_region[1])
start = max(region[0], hq_region[0])
if start >= end:
return None
else:
return (start, end)
def test_zmw_multipart_regions(self):
regions = []
# First read in the regions from the h5 files directly
for filename in self.baxh5_filenames:
with h5py.File(filename, 'r') as f:
region_table = f['PulseData/Regions']
regions.extend(region_table.value.tolist())
# Now see what BasH5Reader reports for regions
reader = pbcore.io.BasH5Reader(self.bash5_filename)
for zmw in reader.allSequencingZmws:
region_table = reader[zmw].regionTable.tolist()
true_regions = [k for k in regions if k[0] == zmw]
true_hq_region = [k for k in true_regions if k[1] == 2][0]
reported_hq_region = reader[zmw].hqRegion
nose.tools.assert_equal(reported_hq_region[0], true_hq_region[2])
nose.tools.assert_equal(reported_hq_region[1], true_hq_region[3])
# Check the reported adapter regions
reported_adapter_regions = reader[zmw].adapterRegions
true_adapter_regions = [k for k in true_regions if k[1] == 0]
region_count = 0
for region in true_adapter_regions:
bound = (region[2], region[3])
clipped_region = self._clip_region(bound, reported_hq_region)
if clipped_region:
nose.tools.assert_in(clipped_region,
reported_adapter_regions)
region_count += 1
nose.tools.assert_equal(region_count, len(reported_adapter_regions))
# And the reported insert regions
reported_insert_regions = reader[zmw].insertRegions
true_insert_regions = [k for k in true_regions if k[1] == 1]
region_count = 0
for region in true_insert_regions:
bound = (region[2], region[3])
clipped_region = self._clip_region(bound, reported_hq_region)
if clipped_region:
nose.tools.assert_in(clipped_region,
reported_insert_regions)
region_count += 1
nose.tools.assert_equal(region_count, len(reported_insert_regions))
class TestBasH5Reader_20(CommonTests, CommonMultiPartTests, ReadIteratorTests):
"""Tests of BasH5Reader against a 2.0 ba[sx].h5 files, consisting of a
bas.h5 file and three bas.h5 files. The bax.h5 files also contain CCS.
"""
def __init__(self):
"""Get the full paths to the bas and bax.h5 files."""
self.bash5_filename = pbcore.data.getBasH5_v20()
self.baxh5_filenames = pbcore.data.getBaxH5_v20()
def test_20_constructor_bash5(self):
# Tests specific to the v2.0 bas.h5 constructor
reader = pbcore.io.BasH5Reader(self.bash5_filename)
nose.tools.assert_true(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_20)
reader.close()
def test_20_constructor_baxh5(self):
# Tests specific to the v2.0 bax.h5 constructor
for filename in self.baxh5_filenames:
reader = pbcore.io.BasH5Reader(filename)
nose.tools.assert_true(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_20)
reader.close()
@nose.tools.raises(ChemistryLookupError)
def test_20_missing_chemistry(self):
"""Tests that we raise an exception when we can't find chemistry information"""
reader = pbcore.io.BasH5Reader(self.bash5_filename)
reader.sequencingChemistry
def test_productivity(self):
"""Test that productivities are set correctly for the ZMW objects."""
productivities = {}
for filename in self.baxh5_filenames:
f = h5py.File(filename, 'r')
hn_to_prod = dict(zip(f["PulseData/BaseCalls/ZMW/HoleNumber"],
f["PulseData/BaseCalls/ZMWMetrics/Productivity"]))
productivities.update(hn_to_prod)
f.close()
reader = pbcore.io.BasH5Reader(self.bash5_filename)
for hn in productivities:
nose.tools.assert_equal(reader[hn].productivity,
productivities[hn])
class TestBasH5Reader_21(CommonTests, CommonMultiPartTests, ReadIteratorTests):
"""Tests of BasH5Reader against a 2.1 ba[sx].h5 files, consisting of a
bas.h5 file and three bas.h5 files. The bax.h5 files do not contain CCS.
"""
def __init__(self):
"""Get the full paths to the bas and bax.h5 files."""
self.bash5_filename = pbcore.data.getBasH5_v21()
self.baxh5_filenames = pbcore.data.getBaxH5_v21()
def test_21_constructor_bash5(self):
# Tests specific to the v2.0 bas.h5 constructor
reader = pbcore.io.BasH5Reader(self.bash5_filename)
nose.tools.assert_false(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_21)
reader.close()
def test_21_constructor_baxh5(self):
# Tests specific to the v2.0 bax.h5 constructor
for filename in self.baxh5_filenames:
reader = pbcore.io.BasH5Reader(filename)
nose.tools.assert_false(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_21)
reader.close()
def test_21_external_region_baxh5(self):
"""Test the optional region file override"""
for baxfile in self.baxh5_filenames:
# Count of the subreads using internal region table
reader = pbcore.io.BaxH5Reader(baxfile)
bax_subread_count = len([x for x in reader.subreads()])
# Count of subreads using external region table
rgnfile = baxfile.replace('bax.h5','rgn.h5')
reader.loadExternalRegions(rgnfile)
rgn_subread_count = len([x for x in reader.subreads()])
nose.tools.assert_true(rgn_subread_count < bax_subread_count)
@nose.tools.raises(ChemistryLookupError)
def test_21_missing_chemistry(self):
"""Tests that we raise an exception when we can't find chemistry information"""
reader = pbcore.io.BasH5Reader(self.bash5_filename)
reader.sequencingChemistry
@nose.tools.raises(IOError)
def test_21_bad_external_region_baxh5(self):
"""Tests that we raise an exception when incorrect region file given"""
baxfiles = self.baxh5_filenames
baxfile = baxfiles[0]
rgnfile = baxfiles[1].replace('bax.h5','rgn.h5')
pbcore.io.BaxH5Reader(baxfile, regionH5Filename=rgnfile)
class TestBasH5Reader_23(CommonTests, CommonMultiPartTests, ReadIteratorTests):
"""Tests of BasH5Reader against a 2.3 ba[sx].h5 files, consisting of a
bas.h5 file and three bas.h5 files. The bax.h5 files do not contain CCS,
but do contain Chemistry information
"""
def __init__(self):
"""Get the full paths to the bas and bax.h5 files."""
self.bash5_filename = pbcore.data.getBasH5_v23()
self.baxh5_filenames = pbcore.data.getBaxH5_v23()
def test_23_constructor_bash5(self):
# Tests specific to the v2.0 bas.h5 constructor
reader = pbcore.io.BasH5Reader(self.bash5_filename)
nose.tools.assert_false(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_23)
nose.tools.assert_equal(reader.sequencingChemistry, 'P6-C4')
reader.close()
def test_23_constructor_baxh5(self):
# Tests specific to the v2.0 bax.h5 constructor
for filename in self.baxh5_filenames:
reader = pbcore.io.BasH5Reader(filename)
nose.tools.assert_false(reader.hasConsensusBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_23)
nose.tools.assert_equal(reader.sequencingChemistry, 'P6-C4')
reader.close()
class TestBasH5Reader_CCS(ReadIteratorTests):
"""Test BasH5Reader with a ccs.h5 file produced by P_CCS."""
def __init__(self):
"""Get the full paths to the bas and bax.h5 files."""
self.bash5_filename = pbcore.data.getCCSH5()
self.baxh5_filenames = []
def test_constructor_ccsh5(self):
# Test that BasH5Reader initializes correctly with a ccs.h5 file
reader = pbcore.io.BasH5Reader(self.bash5_filename)
nose.tools.assert_is_instance(reader.file, h5py.File)
nose.tools.assert_true(reader.hasConsensusBasecalls)
nose.tools.assert_false(reader.hasRawBasecalls)
nose.tools.assert_equal(reader.movieName, pbcore.data.MOVIE_NAME_CCS)
nose.tools.assert_equal(len(reader.parts), 1)
for zmw in reader.sequencingZmws:
nose.tools.assert_in(zmw, reader.allSequencingZmws)
nose.tools.assert_is_instance(reader[zmw], Zmw)
nose.tools.assert_less_equal(len(reader.sequencingZmws),
len(reader.allSequencingZmws))
reader.close()
def test_ccs_zmw(self):
# Test Zmw objects derived from a BasH5Reader reading a ccs.h5
reader = pbcore.io.BasH5Reader(self.bash5_filename)
sequencing_zmws = set(reader.sequencingZmws)
for zmw in reader.allSequencingZmws:
region_table = reader[zmw].regionTable
nose.tools.assert_equal(len(region_table), 1)
nose.tools.assert_equal(region_table[0][0], zmw)
nose.tools.assert_equal(region_table[0][1], 2)
nose.tools.assert_equal(len(reader[zmw].insertRegions), 0)
nose.tools.assert_equal(len(reader[zmw].adapterRegions), 0)
nose.tools.assert_equal(len(reader[zmw].subreads), 0)
with nose.tools.assert_raises(ValueError):
reader[zmw].read()
if zmw in sequencing_zmws:
nose.tools.assert_is_instance(reader[zmw].ccsRead,
CCSZmwRead)
else:
nose.tools.assert_is_none(reader[zmw].ccsRead)
|
