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import os.path as op
import pytest
from pbcore.io import AlignmentSet
from kineticsTools.ipdModel import IpdModel
from kineticsTools import ReferenceUtils
from test_integration import REF_DIR, DATA_DIR
@pytest.mark.internal_data
class TestIpdModel:
@classmethod
def setup_class(cls):
ref_set = op.join(REF_DIR, "ecoli_k12_MG1655_first50k",
"ecoli_k12_MG1655_first50k.referenceset.xml")
alignments = op.join(DATA_DIR, "ecoli_first_50k.mapped.bam")
ds_aln = AlignmentSet(alignments)
contigs = ReferenceUtils.loadReferenceContigs(
ref_set,
alignmentSet=ds_aln)
from kineticsTools.loader import getIpdModelFilename
from kineticsTools.ipdSummary import _getResourcePathSpec
model_file = getIpdModelFilename(
None, "S/P2-C2", [_getResourcePathSpec()])
cls._model = IpdModel(contigs, model_file)
def test_refLength(self):
assert self._model.refLength(0) == 50000
def test_snippetFunc(self):
f = self._model.snippetFunc(0, 5, 5)
assert f(9, 0) == "TTTCATTCTGA"
assert f(9, 1) == "TCAGAATGAAA"
def test_getReferenceWindow(self):
w1 = self._model.getReferenceWindow(0, 0, 4, 15)
assert w1 == "TTTCATTCTGA"
w2 = self._model.getReferenceWindow(0, 1, 4, 15)
assert w2 == "GTCAGAATGAA"
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