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import pytest
import logging
import tempfile
import copy
import os
from collections import Counter
from pbcore.io import SubreadSet, AlignmentSet
from pbcore.io.dataset.DataSetErrors import InvalidDataSetIOError
from pbcore.io.dataset.DataSetMembers import CollectionMetadata
import pbcore.data.datasets as data
from pbcore.io.dataset.DataSetValidator import validateFile
log = logging.getLogger(__name__)
class TestDataSet:
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
# check that we aren't adding any additional biosamples elements:
assert Counter(ds.metadata.tags)['BioSamples'] == 1
assert ds.metadata.bioSamples[0].name == 'consectetur purus'
assert ds.metadata.bioSamples[0].DNABarcodes[0].name == 'F1--R1'
assert ds.metadata.collections[0].getV('children', 'Automation')
assert ds.metadata.collections[0].automation
ds.metadata.collections[0].automation.automationParameters.addParameter(
'foo', 'bar')
assert ds.metadata.collections[0].automation.automationParameters['foo'].value == 'bar'
assert ds.metadata.collections[0].automation.automationParameters.parameterNames == [
None, 'foo']
def test_de_novo(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
log.info(ofn)
ss = SubreadSet(data.getXml(9))
col = CollectionMetadata()
assert not ss.metadata.collections
ss.metadata.collections.append(col)
assert ss.metadata.collections
col.cellIndex = 1
assert ss.metadata.collections[0].cellIndex == '1'
col.instrumentName = "foo"
assert ss.metadata.collections[0].instrumentName == "foo"
col.context = 'bar'
assert ss.metadata.collections[0].context == "bar"
ss.metadata.collections[0].runDetails.name = 'foo'
assert 'foo' == ss.metadata.collections[0].runDetails.name
ss.metadata.collections[0].wellSample.name = 'bar'
assert 'bar' == ss.metadata.collections[0].wellSample.name
ss.metadata.collections[0].wellSample.wellName = 'baz'
assert 'baz' == ss.metadata.collections[0].wellSample.wellName
ss.metadata.collections[0].wellSample.concentration = 'baz'
assert 'baz' == ss.metadata.collections[0].wellSample.concentration
# There are no existing biosamples:
assert not 'BioSamples' in ss.metadata.tags
# Therefore the metadata is falsy
assert not ss.metadata.bioSamples
ss.metadata.bioSamples.addSample('Clown')
assert 'Clown' == ss.metadata.bioSamples[0].name
ss.metadata.bioSamples[0].DNABarcodes.addBarcode('Dentist')
assert 'Dentist' == ss.metadata.bioSamples[0].DNABarcodes[0].name
# check that we are adding one additional biosamples element:
assert Counter(ss.metadata.tags)['BioSamples'] == 1
# Therefore the metadata is truthy
assert ss.metadata.bioSamples
ss.write(ofn, validate=False)
@pytest.mark.internal_data
def test_loadMetadata(self):
aln = AlignmentSet(data.getXml(7))
assert not aln.metadata.collections
aln.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
assert aln.metadata.collections
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
assert not sset.metadata.collections
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
sset.write(fn)
validateFile(fn)
validateFile(sset_fn)
assert sset.metadata == orig_metadata
# load the wrong thing...
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
assert not sset.metadata.collections
with pytest.raises(InvalidDataSetIOError):
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.sts.xml')
def test_uuid(self):
ds = AlignmentSet()
old = ds.uuid
_ = ds.newUuid()
assert not old == ds.uuid
aln = AlignmentSet(data.getXml(7))
oldUuid = aln.uuid
outdir = tempfile.mkdtemp(suffix="dataset-doctest")
outXml = os.path.join(outdir, 'tempfile.xml')
aln.write(outXml)
aln = AlignmentSet(outXml)
assert aln.uuid == oldUuid
@pytest.mark.skip(reason="pbtestdata is not packaged yet")
@pytest.mark.internal_data
def test_merge(self):
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
assert len(sset.metadata.collections) == 1
sset.metadata.collections.merge(orig_metadata.collections)
assert len(sset.metadata.collections) == 2
sset = SubreadSet(sset_fn)
sset.metadata.collections.merge(
orig_metadata.collections, forceUnique=True)
assert len(sset.metadata.collections) == 1
def test_merge_biosamples(self):
import pbtestdata
ds1 = pbtestdata.get_file("subreads-biosample-1")
ds2 = pbtestdata.get_file("subreads-biosample-2")
# Case 1: two biosamples
ds = SubreadSet(ds1, ds2)
samples = [bs.name for bs in ds.metadata.bioSamples]
assert samples == ["Alice", "Bob"]
# Case 2: same biosample in both files
ds = SubreadSet(ds1, ds1)
samples = [bs.name for bs in ds.metadata.bioSamples]
assert samples == ["Alice"]
assert len(ds.metadata.bioSamples[0].DNABarcodes) == 1
# Case 3: same biosample, different barcodes
dsTmp = SubreadSet(ds1)
dsTmp.metadata.bioSamples[0].DNABarcodes[0].name = "F7--R7"
tmpFile = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
dsTmp.write(tmpFile)
ds = SubreadSet(ds1, tmpFile)
samples = [bs.name for bs in ds.metadata.bioSamples]
assert samples == ["Alice"]
bcs = [bc.name for bc in ds.metadata.bioSamples[0].DNABarcodes]
assert bcs == ["F1--R1", "F7--R7"]
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