def setUp(self):
self.sample = Sample(
project_id="project",
sample_id="sample",
sample_prefix="project/sample/sample",
project_prefix="project",
sample_run_prefix="project/sample/samplerun/samplerun")
class TestABCSample(unittest.TestCase):
def setUp(self):
self.sample = Sample(project_id="project", sample_id="sample", sample_prefix="project/sample/sample", project_prefix="project", sample_run_prefix="project/sample/samplerun/samplerun")
def test_sample(self):
self.assertEqual(self.sample.prefix(), "project/sample/sample")
self.assertEqual(self.sample.path(), "project/sample")
self.assertEqual(self.sample.prefix("project"), "project")
self.assertEqual(self.sample.path("project"), ".")
self.assertEqual(self.sample.prefix("sample_run"), "project/sample/samplerun/samplerun")
self.assertEqual(self.sample.path("sample_run"), "project/sample/samplerun")
self.assertEqual(self.sample.project_id(), "project")
class TestABCSample(unittest.TestCase):
def setUp(self):
self.sample = Sample(
project_id="project",
sample_id="sample",
sample_prefix="project/sample/sample",
project_prefix="project",
sample_run_prefix="project/sample/samplerun/samplerun")
def test_sample(self):
self.assertEqual(self.sample.prefix(), "project/sample/sample")
self.assertEqual(self.sample.path(), "project/sample")
self.assertEqual(self.sample.prefix("project"), "project")
self.assertEqual(self.sample.path("project"), ".")
self.assertEqual(self.sample.prefix("sample_run"),
"project/sample/samplerun/samplerun")
self.assertEqual(self.sample.path("sample_run"),
"project/sample/samplerun")
self.assertEqual(self.sample.project_id(), "project")
def setUp(self):
self.sample = Sample(project_id="project", sample_id="sample", sample_prefix="project/sample/sample", project_prefix="project", sample_run_prefix="project/sample/samplerun/samplerun")
def make_fastq_links(targets,
indir,
outdir,
fastq_suffix="001.fastq.gz",
ssheet="SampleSheet.csv"):
"""Given a set of targets and an output directory, create links
from targets (source raw data) to an output directory.
:param targets: list of :class:`ratatosk.experiment.ISample` objects
:param outdir: (top) output directory
:param fastq_suffix: fastq suffix
:param ssheet: sample sheet name
:returns: new targets list with updated output directory
"""
newtargets = []
for tgt in targets:
fastq = glob.glob("{}*{}".format(tgt.prefix("sample_run"),
fastq_suffix))
if len(fastq) == 0:
logger.warn("No fastq files for prefix {} in {}".format(
tgt.prefix("sample_run"), "make_fastq_links"))
for f in fastq:
newpath = os.path.join(outdir, os.path.relpath(f, indir))
if not os.path.exists(os.path.dirname(newpath)):
logger.info("Making directories to {}".format(
os.path.dirname(newpath)))
os.makedirs(os.path.dirname(newpath))
if not os.path.exists(
os.path.join(os.path.dirname(newpath), ssheet)):
try:
os.symlink(
os.path.abspath(
os.path.join(os.path.dirname(f), ssheet)),
os.path.join(os.path.dirname(newpath), ssheet))
except:
logger.warn("No sample sheet found for {}".format())
if not os.path.exists(newpath):
logger.info("Linking {} -> {}".format(newpath,
os.path.abspath(f)))
os.symlink(os.path.abspath(f), newpath)
if not os.path.lexists(
os.path.join(
os.path.dirname(newpath), ssheet)) and os.path.exists(
os.path.abspath(
os.path.join(os.path.dirname(f), ssheet))):
os.symlink(
os.path.abspath(os.path.join(os.path.dirname(f), ssheet)),
os.path.join(os.path.dirname(newpath), ssheet))
newsample = Sample(project_id=tgt.project_id(),
sample_id=tgt.sample_id(),
project_prefix=outdir,
sample_prefix=os.path.join(
outdir,
os.path.relpath(tgt.prefix("sample"), indir)),
sample_run_prefix=os.path.join(
outdir,
os.path.relpath(tgt.prefix("sample_run"),
indir)))
newtargets.append(newsample)
# newtargets.append((tgt.sample_id(),
# os.path.join(outdir, os.path.relpath(tgt.prefix("sample"), indir)),
# os.path.join(outdir, os.path.relpath(tgt.prefix("sample_run"), indir))))
return newtargets
