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 elongation(lib_conds, template_texs, libs, strand, trans,
args_tran, strain, tolers):
'''check coverage and replicate match to form transcript'''
first = True
pre_pos = -1
check_tex = []
tracks = []
conds = {}
pre_wig = None
detect = False
texs = template_texs.copy()
tmp_covers = {"best": 0, "toler": -1}
for cond, lib_tracks in lib_conds.items():
for lib_name, covers in lib_tracks.items():
index_pos = 0
for cover in covers:
for cond, lib_tracks in lib_conds.items():
for lib_track in lib_tracks.keys():
real_track = lib_track.split("|")[-3]
if index_pos < len(lib_tracks[lib_track]):
compare_cover = lib_tracks[lib_track][index_pos]
else:
compare_cover = 0
detect_hight_toler(
compare_cover, args_tran.height,
tmp_covers, tracks, real_track)
for track in tracks:
if len(texs) != 0:
for key, num in texs.items():
if track in key:
texs[key] += 1
check_tex_conds(tracks, libs, texs, check_tex,
conds, args_tran.tex)
for cond, detect_num in conds.items():
if ("tex" in cond):
tex_rep = get_repmatch(args_tran.replicates["tex"], cond)
if detect_num >= tex_rep:
detect = True
elif ("frag" in cond):
frag_rep = get_repmatch(args_tran.replicates["frag"], cond)
if detect_num >= frag_rep:
detect = True
if detect:
detect = False
trans[strain].append(tmp_covers["best"])
else:
trans[strain].append(-1)
if (tmp_covers["toler"] != -1):
tolers.append(tmp_covers["toler"])
else:
tolers.append(args_tran.height + 10)
tmp_covers = {"best": 0, "toler": -1}
tracks = []
conds = {}
check_tex = []
texs = template_texs.copy()
index_pos += 1
break
break
def get_coverage(term, wigs, strand, template_texs, args_term):
'''get proper coverage to check the coverage decrease'''
hl_poss = {"high": 0, "low": 0}
hl_covers = {"high": 0, "low": 0}
term_datas = {}
detect_nums = {}
diff_cover = -1
diff = []
for wig_strain, conds in wigs.items():
if wig_strain == term["strain"]:
for cond, tracks in conds.items():
term_covers = []
term_datas[cond] = []
detect_nums[cond] = 0
for lib_name, covers in tracks.items():
track = lib_name.split("|")[-3]
lib_strand = lib_name.split("|")[-2]
lib_type = lib_name.split("|")[-1]
c_start, c_end = check_start_and_end(
term, args_term, covers)
covers = covers[c_start:c_end]
if strand == "-":
covers = covers[::-1]
coverage2term(covers, term, hl_covers, hl_poss, strand,
term_covers, track, args_term, c_start,
c_end, lib_type)
if len(term_covers) != 0:
tmp_cov, tmp_diff, term_datas[cond], detect_nums[cond] = (
compare_replicates(term_covers, template_texs, cond,
args_term))
if (diff_cover == -1) or (diff_cover < tmp_cov):
diff_cover = tmp_cov
diff = tmp_diff
detect = False
for cond, num in detect_nums.items():
if ("texnotex" in cond):
tex_rep = get_repmatch(args_term.replicates["tex"], cond)
if num >= tex_rep:
detect = True
elif ("frag" in cond):
frag_rep = get_repmatch(args_term.replicates["frag"], cond)
if num >= frag_rep:
detect = True
if detect:
detect = False
if strand == "+":
term["detect_p"] = True
else:
term["detect_m"] = True
return diff_cover, diff, term_datas, detect_nums