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from numpy.testing import (assert_array_almost_equal as ASIM,
assert_array_equal as AEQ)
from nose.tools import (nottest,
assert_raises,
assert_equal as EQ)
from nose import SkipTest
import numpy as np
import bisect
import h5py
from collections import Counter
from pbcore import data
from pbcore.io import BamReader, BaxH5Reader
from pbcore.io.align._BamSupport import UnavailableFeature
from pbcore.sequence import reverseComplement as RC
class TestUnalignedBam(object):
def __init__(self):
self.bam = BamReader (data.getUnalignedBam())
self.bax = BaxH5Reader(data.getBaxForBam())
self.baxRead0 = next(self.bax.subreads())
self.bamRead0 = next(iter(self.bam))
def testInvalidOperations(self):
# These kinds of things presently work. Do we want them to
# fail?
# with assert_raises(UnavailableFeature):
# self.bamRead0.isForwardStrand
# with assert_raises(UnavailableFeature):
# self.bamRead0.tStart
# attempts to get read aligned or oriented
with assert_raises(UnavailableFeature):
self.bamRead0.read(aligned=True, orientation="native")
with assert_raises(UnavailableFeature):
self.bamRead0.read(aligned=False, orientation="genomic")
with assert_raises(UnavailableFeature):
self.bamRead0.read()
with assert_raises(UnavailableFeature):
self.bamRead0.InsertionQV(aligned=True, orientation="native")
with assert_raises(UnavailableFeature):
self.bamRead0.InsertionQV(aligned=False, orientation="genomic")
with assert_raises(UnavailableFeature):
self.bamRead0.InsertionQV()
def testReadAccess(self):
EQ(self.bamRead0.read(aligned=False, orientation="native"), self.baxRead0.basecalls())
def testQvAccess(self):
AEQ(self.bamRead0.SubstitutionQV(aligned=False, orientation="native"), self.baxRead0.SubstitutionQV())
AEQ(self.bamRead0.InsertionQV(aligned=False, orientation="native"), self.baxRead0.InsertionQV())
AEQ(self.bamRead0.DeletionTag(aligned=False, orientation="native"), self.baxRead0.DeletionTag())
def testZmwInfo(self):
# WAT. Need to make these accessors more uniform. This is
# totally crazy.
EQ(self.bamRead0.HoleNumber, self.baxRead0.holeNumber)
EQ(self.bamRead0.qStart, self.baxRead0.readStart)
EQ(self.bamRead0.qEnd, self.baxRead0.readEnd)
def testNames(self):
EQ(self.bamRead0.queryName, self.baxRead0.readName)
def testIpd(self):
"""Check that 'Ipd' feature is recognized correctly."""
pfa = self.bam.baseFeaturesAvailable()
EQ(pfa, frozenset(['Ipd', 'DeletionTag', 'MergeQV', 'SubstitutionQV',
'InsertionQV', 'DeletionQV']))
ipd = self.bamRead0.IPD(aligned=False, orientation="native")
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