def setUp(self):
self.tmp_root = tempfile.mkdtemp()
name = "log.txt"
self.log_file = os.path.join(self.tmp_root, name)
content = ("foo Running bar: ls\n"
"\n"
"bar Running foo: pwd\n")
create_file(self.log_file, content)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
name = "counts_foo.txt.summary"
self.counts_file = os.path.join(self.tmp_root, name)
content = ("Assigned:\t1\t5\n"
"Unassigned_foo:\t1\t1\n"
"Foo\n"
"Unassigned_bar:\t2\t4\n")
create_file(self.counts_file, content)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
good_lane = os.path.join(self.tmp_root, "P1234_101/L003")
bad_lane = os.path.join(self.tmp_root, "P1234_101/L005")
os.makedirs(good_lane)
os.makedirs(bad_lane)
name = "Log.final.out"
self.log_file = os.path.join(good_lane, name)
content = get_star_report_content()
create_file(self.log_file, content)
self.bad_log_file = os.path.join(bad_lane, name)
create_file(self.bad_log_file, "badly | formatted | line")
self.good_lane = report.Lane("L003", self.log_file)
self.bad_lane = report.Lane("L005", self.bad_log_file)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
counts_file = os.path.join(self.tmp_root, "counts_foo.txt.summary")
log_file = os.path.join(self.tmp_root, "trimmostar.log")
lane_dir1 = os.path.join(self.tmp_root, "L001")
lane_dir2 = os.path.join(self.tmp_root, "L002")
star_log1 = os.path.join(lane_dir1, "Log.final.out")
star_log2 = os.path.join(lane_dir2, "Log.final.out")
dirs = [lane_dir1, lane_dir2]
files = [counts_file, log_file, star_log1, star_log2]
for d in dirs:
os.makedirs(d)
for f in files:
create_file(f)
lane1 = report.Lane("L001", star_log=star_log1)
lane2 = report.Lane("L002", star_log=star_log2)
self.sample = report.Sample("foo", log=log_file, counts=counts_file,
lanes=[lane1, lane2])
def create_directory_structure(root, samples):
for sample, lanes in samples.items():
sample_dir = os.path.join(root, sample)
os.makedirs(sample_dir)
for lane in lanes:
lane_dir = os.path.join(sample_dir, lane)
os.makedirs(lane_dir)
create_file(os.path.join(lane_dir, "Log.final.out"))
create_file(os.path.join(sample_dir, "trimmostar.log"))
counts_file = "counts_{0}.txt.summary".format(sample)
create_file(os.path.join(sample_dir, counts_file))
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
project_root = os.path.join(self.tmp_root, "P1234_101")
lane_dir = os.path.join(project_root, "L001")
os.makedirs(lane_dir)
trimmo_log = os.path.join(project_root, "trimmostar.log")
counts = os.path.join(project_root, "counts_P1234_101.txt.summary")
star_log_file = os.path.join(lane_dir, "Log.final.out")
create_file(star_log_file, get_star_report_content())
lanes = [report.Lane("L001", star_log_file)]
self.sample = report.Sample("P1234_101", log=trimmo_log,
counts=counts, lanes=lanes)
log_content = ("foo Running bar: ls\n"
"\n"
"bar Running foo: pwd\n")
create_file(trimmo_log, log_content)
counts_content = ("Assigned:\t1\n"
"Unassigned_foo:\t1\n"
"Foo\n"
"Unassigned_bar:\t4\n")
create_file(counts, counts_content)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
star_log = os.path.join(self.tmp_root, "Log.final.out")
create_file(star_log)
self.lane = report.Lane("L001", star_log=star_log)
