class AssetsDifferentialExpression(core.AssetsStep):
Source = core.assetfactory('Source', [
core.AssetAttr('counttable_fn', CSVFile, ''),
core.AssetAttr('sampleinfo_fn', File, '')
])
Target = core.assetfactory('Target',
[core.AssetAttr('diffexp_fn', File, '')])
class Assets(core.AssetsStep):
"""
Assets for :class:`SamtoolsExtractUnaligned`
"""
Source = core.assetfactory('Source', [core.AssetAttr('bamfile', BAMFile, '')])
Target = core.assetfactory('Target', [core.AssetAttr('unaligned', BAMFile, '')])
class AssetsQuantifier(core.AssetsStep):
Source = core.assetfactory('Source', [
core.AssetAttr('alignedreads', BAMFile, ''),
core.AssetAttr('annotationfile', GFFFile, '')
])
Target = core.assetfactory('Target',
[core.AssetAttr('counts', CSVFile, '')])
def test_get_assets(self):
model = core.Model(
tuple()) # getting away with an empty model for this step
cache = self.cls_to_test(self.cache_file.name,
model,
force_create=True)
class Activities(core.Enum):
DATETIME = 'Give date/time'
PythonTime = self.PythonTime
python = PythonTime('python')
stepvariant_db_id = cache.id_step_variant(python,
(Activities.DATETIME, ))
# 2-elements sources
SrcCls = core.assetfactory('Source', [
core.AssetAttr('reference', rnaseq.FASTAFile, ''),
core.AssetAttr('otherreference', rnaseq.FASTAFile, ''),
core.AssetAttr('listoffiles', rnaseq.CSVFileSequence, '')
])
sources = SrcCls(
rnaseq.FASTAFile('foo.fasta'), rnaseq.FASTAFile('bar.fasta'),
rnaseq.CSVFileSequence(
(rnaseq.CSVFile('baz.csv'), rnaseq.CSVFile('baz2.csv'))))
targets = core.AssetSet() # targets
parameters = tuple()
db_id = cache.id_stepconcrete(stepvariant_db_id.id, sources, targets,
parameters)
for storedthing in cache.get_srcassets(db_id.id):
thing = storedthing.resurrect(rnaseq)
class AssetsSplit(core.AssetsStep):
Source = core.assetfactory('Source',
[core.AssetAttr('file', core.File, '')])
Target = core.assetfactory('Target', [
core.AssetAttr('head', core.File, ''),
core.AssetAttr('tail', core.File, '')
])
def test_AssetSet_repr(self):
values = (('abc', ), ('123', '456'))
AssetSet = core.assetfactory('AssetSet', [
core.AssetAttr('afile', core.File, ''),
core.AssetAttr('asequenceoffiles', core.FileSequence, '')
])
assetset = unifex.build_AssetSet(AssetSet, values)
res = str(assetset)
self.assertTrue(isinstance(res, str))
class Assets(core.AssetsStep):
Source = core.assetfactory('Source', [core.AssetAttr('annotation_gtf',
GFFFile, ''),
core.AssetAttr('genome_dir',
FilePattern, ''),
core.AssetAttr('parameters',
FluxSimulatorParameters, '')])
Target = core.assetfactory('Target', [core.AssetAttr('parameters_and_pro',
FluxSimulatorParametersAndPro, '')])
class Assets(core.AssetsStep):
"""
Assets for :class:`BedtoolsBamToFastq`
"""
Source = core.assetfactory('Source',
[core.AssetAttr('bamfile', BAMFile, '')])
Target = core.assetfactory(
'Target', [core.AssetAttr('fastqfile', FASTQFile, '')])
class Assets(core.AssetsStep):
"""
Assets for :class:`SamtoolsBamToSam`
"""
Source = core.assetfactory('Source',
[core.AssetAttr('bamfile', BAMFile, '')])
Target = core.assetfactory('Target',
[core.AssetAttr('samfile', SAMFile, '')])
class AssetsIndexer(core.AssetsStep):
"""
Assets for a general indexing step.
"""
Source = core.assetfactory('Source',
[core.AssetAttr('reference',
FASTAFile, '')])
Target = core.assetfactory('Target',
[core.AssetAttr('indexfilepattern',
FilePattern, '')])
class Assets(core.AssetsStep):
Source = core.assetfactory('Source', [
core.AssetAttr('file', railroadtracks.model.files.CSVFile,
'')
])
Target = core.assetfactory('Target', [
core.AssetAttr('head', railroadtracks.model.files.CSVFile,
''),
core.AssetAttr('tail', railroadtracks.model.files.CSVFile,
'')
])
class Assets(core.AssetsStep):
Source = core.assetfactory('Target', [core.AssetAttr('parameters_and_pro',
FluxSimulatorParametersAndPro, '')])
Target = core.assetfactory('Target', [core.AssetAttr('parameters_and_pro',
FluxSimulatorParametersAndPro, ''),
core.AssetAttr('read1',
FASTQPossiblyGzipCompressed, ''),
core.AssetAttr('read2',
FASTQPossiblyGzipCompressed, ''),
core.AssetAttr('lib',
File, '')])
def test_assetfactory(self):
Foo = core.assetfactory('Foo', [core.AssetAttr('bar', core.File, '')])
# check that the asset bar is defined
foo = Foo(core.File(''))
# check that an incorrect type raises an error
self.assertRaises(AssertionError, Foo, 123)
self.assertTrue(foo.bar._defined)
# check that incorrect parameters make it fail
self.assertRaises(AssertionError, core.assetfactory, 'Foo',
[core.AssetAttr('bar', core.File, None)])
# check that trying to modify an asset raises an error
self.assertRaises(AttributeError, setattr, foo, 'bar', 123)
class Assets(AssetsQuantifier):
Source = core.assetfactory('Source', [
SailfishIndex.Assets.Target.getassetattr('indexfilepattern'),
core.AssetAttr('read1', FASTQPossiblyGzipCompressed, ''),
core.AssetAttr(
'read2', FASTQPossiblyGzipCompressed, '', allownone=True)
])
# 'counts' is coming from QuantifierAbstract
Target = core.assetfactory('Target', [
core.AssetAttr('counts', CSVFile, ''),
core.AssetAttr('output_dir', FilePattern, '')
])
def test_assetfactory_allownone(self):
# check that allownone=True allows unspecified assets
Foo = core.assetfactory(
'Foo', [core.AssetAttr('bar', core.File, '', allownone=True)])
# check that the asset bar is defined
foo = Foo(core.File(''))
self.assertTrue(foo.bar._defined)
# check that an incorrect type raises an error
self.assertRaises(AssertionError, Foo, 123)
foo = Foo(None)
self.assertTrue(foo.bar is None)
# check that trying to modify an asset raises an error
self.assertRaises(AttributeError, setattr, foo, 'bar', 123)
def test_createundefined(self):
# -- createundefined-begin
Foo = core.assetfactory('Foo', [core.AssetAttr('bar', core.File, '')])
# create an undefined set of assets of type Foo
undefoo = Foo.createundefined()
# -- createundefined-end
self.assertTrue(isinstance(undefoo, Foo))
# check that the asset bar is an undefined "saved entity"
self.assertFalse(undefoo.bar._defined)
# check that trying to modify an asset raises an error
# (modifying an asset value will be possible though)
self.assertRaises(AttributeError, setattr, undefoo, 'bar', 123)
undefoo.bar.name = '123'
self.assertEqual('123', undefoo.bar.name)
def test_build_AssetSet(self):
values = (('abc', ), ('123', '456'))
AssetSet = core.assetfactory('AssetSet', [
core.AssetAttr('afile', core.File, ''),
core.AssetAttr('asequenceoffiles', core.FileSequence, '')
])
assetset = unifex.build_AssetSet(AssetSet, values)
#FIXME: where is the test ?
#FIXME: how are allownone=True assets handled ?
# values not allowed to be None cannot be None
values = (None, ('123', '456'))
self.assertRaises(AssertionError, unifex.build_AssetSet, AssetSet,
values)
values = (('abc', ), ('123', '456'))
AssetSet = core.assetfactory('AssetSet', [
core.AssetAttr('afile', core.File, '', allownone=True),
core.AssetAttr('asequenceoffiles', core.FileSequence, '')
])
assetset = unifex.build_AssetSet(AssetSet, values)
values = (None, ('123', '456'))
assetset = unifex.build_AssetSet(AssetSet, values)
class AssetsSorter(core.AssetsStep):
Source = core.assetfactory('Source',
[core.AssetAttr('alignedreads', BAMFile, '')])
Target = core.assetfactory('Target',
[core.AssetAttr('sortedbam', BAMFile, '')])
class Assets(AssetsAligner):
Source = core.assetfactory('Source', [core.AssetAttr('indexfilepattern', BWAIndexFiles, ''),
core.AssetAttr('read1', FASTQPossiblyGzipCompressed, ''),
core.AssetAttr('read2', FASTQPossiblyGzipCompressed, '', allownone=True)])
class Assets(AssetsIndexer):
Target = core.assetfactory('Target',
[core.AssetAttr('indexfilepattern',
BWAIndexFiles, '')])
class AssetsAligner(core.AssetsStep):
Source = core.assetfactory('Source', [core.AssetAttr('indexfilepattern', FilePattern, ''),
core.AssetAttr('read1', FASTQPossiblyGzipCompressed, ''),
core.AssetAttr('read2', FASTQPossiblyGzipCompressed, '', allownone=True)])
Target = core.assetfactory('Target', [core.AssetAttr('alignment', BAMFile, '')])
class Assets(TopHat.Assets):
Source = core.assetfactory('Source', [core.AssetAttr('indexfilepattern', SavedBowtie2Index, ''),
core.AssetAttr('read1', FASTQPossiblyGzipCompressed, ''),
core.AssetAttr('read2', FASTQPossiblyGzipCompressed, '', allownone=True)])
class Assets(BedtoolsBamToFastq.Assets):
Target = core.assetfactory('Target', [
core.AssetAttr('fastqfile', FASTQFile, ''),
core.AssetAttr('fastqfile2', FASTQFile, '')
])
class Assets(core.AssetsStep):
Source = core.assetfactory('Source', [core.AssetAttr('parameters_and_pro',
FluxSimulatorParametersAndPro, '')])
Target = core.assetfactory('Target', [core.AssetAttr('parameters_and_pro',
FluxSimulatorParametersAndPro, '')])
def test_AssetStep_NoTarget(self):
Foo = core.assetfactory('Foo', [core.AssetAttr('bar', core.File, '')])
# no target
assetset = core.AssetsStep(Foo)
self.assertTrue(isinstance(assetset.__str__(), str))
def test_AssetStep_Target(self):
Foo = core.assetfactory('Foo', [core.AssetAttr('bar', core.File, '')])
Bar = core.assetfactory('Bar', [core.AssetAttr('foo', core.File, '')])
assetset = core.AssetsStep(Foo, Bar)
self.assertTrue(isinstance(assetset.__str__(), str))
class Assets(AssetsAligner):
Target = core.assetfactory('Target', [core.AssetAttr('alignment', BAMFile, '')])
class AssetsCat(core.AssetsStep):
Source = core.assetfactory(
'Source', [core.AssetAttr('heads', core.FileSequence, '')])
Target = core.assetfactory('Target',
[core.AssetAttr('result', core.File, '')])
class Assets(AssetsIndexer):
Target = core.assetfactory('Target',
[core.AssetAttr('indexfilepattern',
SavedBowtieIndex, '')])
def test_id_stepconcrete(self):
model = core.Model(
tuple()) # getting away with an empty model for this step
cache = self.cls_to_test(self.cache_file.name,
model,
force_create=True)
class Activities(core.Enum):
DATETIME = 'Give date/time'
PythonTime = self.PythonTime
python = PythonTime('python')
stepvariant_db_id = cache.id_step_variant(python,
(Activities.DATETIME, ))
# empty sources is a special case
sources = core.AssetSet() # source
targets = core.AssetSet() # targets
parameters = tuple()
db_id = cache.id_stepconcrete(stepvariant_db_id.id, sources, targets,
parameters)
db_id_same = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertEqual(db_id.id, db_id_same.id)
db_id_notthesame = cache.id_stepconcrete(stepvariant_db_id.id,
sources,
targets,
parameters,
tag=2)
self.assertNotEqual(db_id.id, db_id_notthesame.id)
# 1-element sources
sources = railroadtracks.model.aligners.AssetsIndexer.Source(
rnaseq.FASTAFile('foo.fasta'))
db_id_nothesame = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertNotEqual(db_id.id, db_id_nothesame.id)
db_id_sameagain = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertEqual(db_id_sameagain.id, db_id_nothesame.id)
db_id_nothesameagain = cache.id_stepconcrete(stepvariant_db_id.id,
sources, targets,
("%Y", ))
self.assertNotEqual(db_id.id, db_id_nothesameagain.id)
self.assertNotEqual(db_id_sameagain.id, db_id_nothesameagain.id)
# 1-element sources, several parameters
db_id_2params = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, ("%Y", "Z"))
db_id_same2params = cache.id_stepconcrete(stepvariant_db_id.id,
sources, targets,
("%Y", "Z"))
self.assertEqual(db_id_2params.id, db_id_same2params.id)
db_id_2otherparams = cache.id_stepconcrete(stepvariant_db_id.id,
sources, targets,
("%Y", "W"))
self.assertNotEqual(db_id_2params.id, db_id_2otherparams.id)
# 2-elements sources
SrcCls = core.assetfactory('Source', [
core.AssetAttr('reference', rnaseq.FASTAFile, ''),
core.AssetAttr('otherreference', rnaseq.FASTAFile, '')
])
sources = SrcCls(rnaseq.FASTAFile('foo.fasta'),
rnaseq.FASTAFile('bar.fasta'))
db_id_notthesame = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertNotEqual(db_id.id, db_id_notthesame.id)
db_id_sameagain = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertEqual(db_id_sameagain.id, db_id_notthesame.id)
# 1-element source / 1-element target
sources = railroadtracks.model.aligners.AssetsIndexer.Source(
rnaseq.FASTAFile('foo.fasta'))
targets = railroadtracks.model.aligners.AssetsIndexer.Target(
rnaseq.FilePattern('foo_idx'))
foo_sh = rnaseq.Anyscript()
stepvariant_db_id = cache.id_step_variant(foo_sh,
(Activities.DATETIME, ))
db_id_nothesame = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertNotEqual(db_id.id, db_id_nothesame.id)
db_id_sameagain = cache.id_stepconcrete(stepvariant_db_id.id, sources,
targets, parameters)
self.assertEqual(db_id_sameagain.id, db_id_nothesame.id)
# fail if target assets are suddenly different
targets_bar = railroadtracks.model.aligners.AssetsIndexer.Target(
rnaseq.FilePattern('bar_idx'))
self.assertRaises(ValueError, cache.id_stepconcrete,
stepvariant_db_id.id, sources, targets_bar,
parameters)
