def test_check_tex(self):
template_texs = self.example.texs
covers = self.example.cover_datas
coverages = {"3utr": 100, "5utr": 600}
poss = {"high": 30, "low": 10}
median = {"track1_tex": {"median": 100, "mean": 200}, "track1_notex": {"median": 30, "mean": 80},
"track2_tex": {"median": 150, "mean": 200}, "track2_notex": {"median": 10, "mean": 20},
"frag": {"median": 80, "mean": 100}}
target_datas = []
texs = {"track1_tex@AND@track1_notex": 0, "track2_tex@AND@track2_notex": 0}
detect_num_lib = cover_detect.check_tex(template_texs, covers, target_datas, 20, None, poss, median,
coverages, "3utr", 200, 2)
self.assertEqual(detect_num_lib, 2)
num_frag = 0
num_tex = 0
for target in target_datas:
if target["type"] == "frag":
num_frag += 1
else:
num_tex += 1
self.assertEqual(num_frag, 1)
self.assertEqual(num_tex, 2)
detect_num_lib = cover_detect.check_tex(template_texs, covers, target_datas, 20, "sRNA_utr_derived",
poss, median, coverages, "5utr", 200, 2)
self.assertEqual(detect_num_lib, 2)
self.assertDictEqual(poss, {'start': 100, 'high': 30, 'end': 202, 'low': 10})
def test_check_tex(self):
template_texs = self.example.texs
covers = self.example.cover_datas
coverages = {"3utr": 100, "5utr": 600}
poss = {"high": 30, "low": 10}
median = {"track1_tex": {"median": 100, "mean": 200}, "track1_notex": {"median": 30, "mean": 80},
"track2_tex": {"median": 150, "mean": 200}, "track2_notex": {"median": 10, "mean": 20},
"frag": {"median": 80, "mean": 100}}
target_datas = []
texs = {"track1_tex@AND@track1_notex": 0, "track2_tex@AND@track2_notex": 0}
detect_num_lib = cover_detect.check_tex(template_texs, covers, target_datas, 20, None, poss, median,
coverages, "3utr", 200, 2)
self.assertEqual(detect_num_lib, 2)
num_frag = 0
num_tex = 0
for target in target_datas:
if target["type"] == "frag":
num_frag += 1
else:
num_tex += 1
self.assertEqual(num_frag, 1)
self.assertEqual(num_tex, 2)
detect_num_lib = cover_detect.check_tex(template_texs, covers, target_datas, 20, "sRNA_utr_derived",
poss, median, coverages, "5utr", 200, 2)
self.assertEqual(detect_num_lib, 2)
self.assertDictEqual(poss, {'start': 100, 'high': 30, 'end': 202, 'low': 10})
def compare_replicates(term_covers, template_texs, cond, args_term):
'''check the cutoff of replicate match'''
detect_num = 0
term_datas = []
diff_cover = -1
diff = []
detect = False
detect_num = check_tex(template_texs, term_covers, term_datas, None,
"terminator", None, None, None, None, 0,
args_term.tex_notex)
if ("texnotex" in cond):
tex_rep = get_repmatch(args_term.replicates["tex"], cond)
if detect_num >= tex_rep:
detect = True
elif ("frag" in cond):
frag_rep = get_repmatch(args_term.replicates["frag"], cond)
if detect_num >= frag_rep:
detect = True
if detect:
detect = False
for term in term_datas:
if (len(diff) == 0) or (diff_cover < term["diff"]):
diff_cover = term["diff"]
diff = term
return diff_cover, diff, term_datas, detect_num
def compare_replicates(term_covers, template_texs, cond, args_term):
'''check the cutoff of replicate match'''
detect_num = 0
term_datas = []
diff_cover = -1
diff = []
detect = False
detect_num = check_tex(template_texs, term_covers, term_datas, None,
"terminator", None, None, None, None, 0,
args_term.tex_notex)
if ("texnotex" in cond):
tex_rep = get_repmatch(args_term.replicates["tex"], cond)
if detect_num >= tex_rep:
detect = True
elif ("frag" in cond):
frag_rep = get_repmatch(args_term.replicates["frag"], cond)
if detect_num >= frag_rep:
detect = True
if detect:
detect = False
for term in term_datas:
if (len(diff) == 0) or (diff_cover < term["diff"]):
diff_cover = term["diff"]
diff = term
return diff_cover, diff, term_datas, detect_num
def compare_replicates(term_covers, template_texs, cond, args_term):
detect_num = 0
term_datas = []
diff_cover = -1
diff = []
detect_num = check_tex(template_texs, term_covers, term_datas, None,
"terminator", None, None, None, None, 0,
args_term.tex_notex)
if ((detect_num >= args_term.replicates["tex"]) and
("texnotex" in cond)) or ((detect_num >= args_term.replicates["frag"])
and ("frag" in cond)):
for term in term_datas:
if (len(diff) == 0) or (diff_cover < term["diff"]):
diff_cover = term["diff"]
diff = term
return diff_cover, diff, term_datas, detect_num
def compare_replicates(term_covers, template_texs, cond, args_term):
detect_num = 0
term_datas = []
diff_cover = -1
diff = []
detect_num = check_tex(template_texs, term_covers, term_datas, None,
"terminator", None, None, None, None, 0,
args_term.tex_notex)
if ((detect_num >= args_term.replicates["tex"]) and (
"texnotex" in cond)) or (
(detect_num >= args_term.replicates["frag"]) and (
"frag" in cond)):
for term in term_datas:
if (len(diff) == 0) or (diff_cover < term["diff"]):
diff_cover = term["diff"]
diff = term
return diff_cover, diff, term_datas, detect_num