def read_wig(filename, strand, libs):
wig_parser = WigParser()
wigs = {}
if filename is not False:
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.strain not in wigs.keys():
wigs[entry.strain] = {}
for lib in libs:
if lib["cond"] not in wigs[entry.strain]:
wigs[entry.strain][lib["cond"]] = {}
for lib in libs:
if (lib["name"] == entry.track) and (
lib["strand"] == entry.strand):
lib_name = "|".join([
entry.track, entry.strand, lib["type"]])
if lib_name not in wigs[entry.strain][lib["cond"]].keys():
wigs[entry.strain][lib["cond"]][lib_name] = []
wigs[entry.strain][lib["cond"]][lib_name].append(entry.coverage)
wig_fh.close()
for strain, conds in wigs.items():
for cond, lib_names in conds.items():
for lib_name, cover_list in lib_names.items():
wigs[strain][cond][lib_name] = np.array(
wigs[strain][cond][lib_name])
return wigs
def read_wig(filename, strand, libs):
wig_parser = WigParser()
wigs = {}
if filename is not False:
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.strain not in wigs.keys():
strain = entry.strain
wigs[strain] = {}
for lib in libs:
if lib["cond"] not in wigs[strain]:
wigs[strain][lib["cond"]] = {}
for lib in libs:
if (lib["name"] == entry.track) and (lib["strand"]
== entry.strand):
lib_name = "|".join(
[entry.track, entry.strand, lib["type"]])
if lib_name not in wigs[strain][lib["cond"]].keys():
wigs[strain][lib["cond"]][lib_name] = []
wigs[strain][lib["cond"]][lib_name].append(entry.coverage)
wig_fh.close()
for strain, conds in wigs.items():
for cond, lib_names in conds.items():
for lib_name, cover_list in lib_names.items():
wigs[strain][cond][lib_name] = np.array(
wigs[strain][cond][lib_name])
return wigs
class TestParserWig(unittest.TestCase):
def setUp(self):
self.example = Example()
self.wig_parser = WigParser()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_parser(self):
wigs = []
wig_f_fh = StringIO(self.example.wig_forward_file)
for entry in self.wig_parser.parser(wig_f_fh, "+"):
self.assertEqual(entry.strain, "aaa")
self.assertEqual(entry.track, "TSB_t0_TEX_forward")
wigs.append(entry)
self.assertEqual(wigs[2].pos, 3)
self.assertEqual(wigs[2].coverage, 1.4041251228308191)
wigs = []
wig_r_fh = StringIO(self.example.wig_reverse_file)
for entry in self.wig_parser.parser(wig_r_fh, "-"):
self.assertEqual(entry.strain, "aaa")
self.assertEqual(entry.track, "TSB_t0_TEX_reverse")
wigs.append(entry)
self.assertEqual(wigs[2].pos, 3)
self.assertEqual(wigs[2].coverage, 1.4041251228308191)
class TestParserWig(unittest.TestCase):
def setUp(self):
self.example = Example()
self.wig_parser = WigParser()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_parser(self):
wigs = []
wig_f_fh = StringIO(self.example.wig_forward_file)
for entry in self.wig_parser.parser(wig_f_fh, "+"):
self.assertEqual(entry.strain, "aaa")
self.assertEqual(entry.track, "TSB_t0_TEX_forward")
wigs.append(entry)
self.assertEqual(wigs[2].pos, 3)
self.assertEqual(wigs[2].coverage, 1.4041251228308191)
wigs = []
wig_r_fh = StringIO(self.example.wig_reverse_file)
for entry in self.wig_parser.parser(wig_r_fh, "-"):
self.assertEqual(entry.strain, "aaa")
self.assertEqual(entry.track, "TSB_t0_TEX_reverse")
wigs.append(entry)
self.assertEqual(wigs[2].pos, 3)
self.assertEqual(wigs[2].coverage, 1.4041251228308191)
def import_wig(lib, wigs, strand):
wig_parser = WigParser()
for wig in lib:
wigs[wig] = {}
strain = ""
wig_fh = open(wig)
for entry in wig_parser.parser(wig_fh, strand):
if strain != entry.strain:
wigs[wig][entry.strain] = []
strain = entry.strain
wigs[wig][strain].append(entry)
wig_fh.close()
def import_wig(lib, wigs, strand):
wig_parser = WigParser()
for wig in lib:
wigs[wig] = {}
strain = ""
wig_fh = open(wig)
for entry in wig_parser.parser(wig_fh, strand):
if strain != entry.strain:
wigs[wig][entry.strain] = []
strain = entry.strain
wigs[wig][strain].append(entry)
wig_fh.close()
def read_wig(filename, strand):
wigs = {}
wig_parser = WigParser()
if filename:
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.strain not in wigs.keys():
strain = entry.strain
wigs[strain] = {}
if entry.track not in wigs[strain].keys():
wigs[strain][entry.track] = []
wigs[strain][entry.track].append({
"pos": entry.pos, "coverage": entry.coverage,
"strand": entry.strand})
wig_fh.close()
return wigs
def read_wig(filename, strand):
wigs = {}
wig_parser = WigParser()
if filename:
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.strain not in wigs.keys():
strain = entry.strain
wigs[strain] = {}
if entry.track not in wigs[strain].keys():
wigs[strain][entry.track] = []
wigs[strain][entry.track].append({
"pos": entry.pos, "coverage": entry.coverage,
"strand": entry.strand})
wig_fh.close()
return wigs
def read_wig(filename, strand, libs):
wig_parser = WigParser()
wigs = {}
if filename is not False:
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.strain not in wigs.keys():
strain = entry.strain
wigs[strain] = {}
for lib in libs:
if lib["cond"] not in wigs[strain]:
wigs[strain][lib["cond"]] = {}
for lib in libs:
if (lib["name"] == entry.track) and (
lib["strand"] == entry.strand):
if entry.track not in wigs[strain][lib["cond"]].keys():
wigs[strain][lib["cond"]][entry.track] = []
wigs[strain][lib["cond"]][entry.track].append({
"pos": entry.pos, "coverage": entry.coverage,
"strand": entry.strand, "type": lib["type"]})
wig_fh.close()
return wigs
def read_wig(filename, libs, strand):
wigs = {}
tracks = []
wig_parser = WigParser()
wig_fh = open(filename)
for entry in wig_parser.parser(wig_fh, strand):
if entry.track not in tracks:
tracks.append(entry.track)
if entry.strain not in wigs.keys():
strain = entry.strain
wigs[entry.strain] = []
for lib in libs:
if strand == lib["strand"]:
for key, value in lib.items():
if (key == "name") and (value == entry.track):
cond = lib["cond"]
track = value
wigs[strain].append({
"pos": entry.pos, "coverage": entry.coverage,
"strand": entry.strand, "track": track,
"cond": cond})
break
wig_fh.close()
return wigs
def setUp(self):
self.example = Example()
self.wig_parser = WigParser()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def setUp(self):
self.example = Example()
self.wig_parser = WigParser()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
