def test_RecipeSimpleIncremental(self):
project = self.project
env = self.env
nsamples = self.nsamples
samplereads = self.samplereads
sampleinfo_fh = self.sampleinfo_fh
reference_fn = self.reference_fn
referenceannotation = self.referenceannotation
PHAGEFASTA = self._PHAGEFASTA
PHAGEGFF = self._PHAGEGFF
# steps used
bowtie2index = env.activities.INDEX.bowtie2build
bowtie2align = env.activities.ALIGN.bowtie2
htseqcount = env.activities.QUANTIFY.htseqcount
merge = env.activities.UTILITY.columnmerger
edger = env.activities.DIFFEXP.edger
from railroadtracks import easy
# sequence of tasks to run
torun = list()
# index for alignment
Assets = bowtie2index.Assets
assets = Assets(Assets.Source(rnaseq.FASTAFile(reference_fn)),
Assets.Target.createundefined())
task_index = project.add_task(bowtie2index,
assets)
# the step is not done
self.assertEqual(hortator._TASK_TODO, task_index.info[1])
torun.append(task_index)
# run the tasks
for task in torun:
# run only if not done
if task.info[1] != hortator._TASK_DONE:
task.execute()
task.status = hortator._TASK_DONE
self.assertEqual(1, project.persistent_graph.nconcrete_steps)
# now that the tasks have run let's open the same project
project_same = easy.Project(project.model, wd=project.wd)
# index for alignment
Assets = bowtie2index.Assets
assets = Assets(Assets.Source(rnaseq.FASTAFile(reference_fn)),
Assets.Target.createundefined())
task_index_same = project_same.add_task(bowtie2index,
assets)
self.assertNotEqual(task_index, task_index_same)
self.assertNotEqual(task_index.call.assets, task_index_same.call.assets)
self.assertListEqual(list(task_index.call.assets.source.reference),
list(task_index_same.call.assets.source.reference))
self.assertListEqual(list(task_index.call.assets.target.indexfilepattern),
list(task_index_same.call.assets.target.indexfilepattern))
self.assertEqual(hortator._TASK_DONE, task_index_same.info[1])
self.assertEqual(1, project.persistent_graph.nconcrete_steps)
def setUp(self):
wd = tempfile.mkdtemp()
self.wd2 = tempfile.mkdtemp()
self.project = easy.Project(rnaseq, wd)
bowtie2index = rnaseq.Bowtie2Build()
reference_fn = PHAGEFASTA
Assets = bowtie2index.Assets
task = self.project.add_task(
bowtie2index,
Assets(Assets.Source(rnaseq.FASTAFile(reference_fn))))
self.task = task
def testAddTaskDifferentProject(self):
project2 = easy.Project(rnaseq, self.wd2)
bowtie2index = rnaseq.Bowtie2Build()
reference_fn = PHAGEFASTA
Assets = bowtie2index.Assets
task2 = project2.add_task(
bowtie2index,
Assets(Assets.Source(rnaseq.FASTAFile(reference_fn))))
#
tsg = tasksetgraph.TaskSetGraph()
tsg.add(self.task)
self.assertRaises(ValueError, tsg.add, task2)
def _project_status_str(args):
import importlib
model = importlib.import_module(args.model)
project = easy.Project(model, args.wd, db_fn=args.db_fn)
if args.follow:
import curses
import sys
try:
curses.wrapper(_project_status_curses,
project,
checkinterval=args.checkinterval)
except KeyboardInterrupt:
sys.exit(1)
else:
print(easy.str_project_view(project))
def setUp(self):
# -- recipe-init-begin
# -- initialization boiler plate code
wd = tempfile.mkdtemp()
project = easy.Project(rnaseq, wd=wd)
# declare the 3rd-party command-line tools we will use
env = easy.Environment(rnaseq)
# -- recipe-init-end
# -- recipe-data-begin
# Phage genome shipped with the package for testing purposes
PHAGEFASTA = railroadtracks.model.simulate.PHAGEFASTA
PHAGEGFF = railroadtracks.model.simulate.PHAGEGFF
# create random data for 6 samples (just testing here)
nsamples = 6
samplereads = list()
with open(PHAGEFASTA) as fasta_fh:
reference = next(railroadtracks.model.simulate.readfasta_iter(fasta_fh))
for sample_i in range(nsamples):
read1_fh = tempfile.NamedTemporaryFile(prefix='read1', suffix='.fq')
read2_fh = tempfile.NamedTemporaryFile(prefix='read2', suffix='.fq')
read1_fh, read2_fh = railroadtracks.model.simulate.randomPEreads(read1_fh,
read2_fh,
reference)
samplereads.append((read1_fh, read2_fh))
sampleinfo_fh = tempfile.NamedTemporaryFile(suffix='.csv', mode='w+')
csv_w = csv.writer(sampleinfo_fh)
csv_w.writerow(['sample_id', 'group'])
for i in range(6):
csv_w.writerow([str(i), ('A','B')[i%2]])
sampleinfo_fh.flush()
referenceannotation = rnaseq.GFFFile(PHAGEGFF)
# -- recipe-data-end
self._wd = wd
self.project = project
self.reference_fn = PHAGEFASTA
self.env = env
self.nsamples = nsamples
self.samplereads = samplereads
self.sampleinfo_fh = sampleinfo_fh
self.referenceannotation = referenceannotation
self._PHAGEFASTA = PHAGEFASTA
self._PHAGEGFF = PHAGEGFF