def merge_star_qc_for_paplot(files, ids, output_file, config, extract = False):
def formatt (input_path):
header = []
value = []
for line in open(input_path):
cells = line.rstrip().split("|")
if len(cells) < 2:
continue
header.append(cells[0].strip(" ").rstrip(" "))
value.append(cells[1].strip().replace("%", ""))
return {"header": "\t".join(header), "value": "\t".join(value)}
import os
for file_path in files:
if os.path.exists(file_path) == False:
print ("[ERROR] file is not exist. %s" % file_path)
files.remove(file_path)
continue
if len(files) == 0:
return
# write meta-data to file
option = subcode_merge._load_option("starqc", config)
meta_text = subcode_merge._merge_metadata(files, option)
f = open(output_file + ".tmp", mode = "w")
if len(meta_text) > 0:
f.write(meta_text + "\n")
for idx in range(len(files)):
data = formatt(files[idx])
if (idx == 0):
f.write("id\t" + data["header"] + "\n")
f.write(ids[idx] + "\t" + data["value"] + "\n")
f.close()
os.rename(output_file + ".tmp", output_file)
def merge_mutaion_for_paplot(files, ids, output_file, config, extract = False):
def calc_map(header, all_header):
mapper = [-1]*len(all_header)
for i in range(len(all_header)):
if all_header[i] in header:
mapper[i] = header.index(all_header[i])
else:
mapper[i] = -1
return mapper
import os
mode = "mutation"
for file_path in files:
if os.path.exists(file_path) == False:
print ("[ERROR] file is not exist. %s" % file_path)
files.remove(file_path)
continue
if len(files) == 0:
return
option = subcode_merge._load_option(mode, config)
if option["header"] == False:
print ("[ERROR] header is necessary for this function.")
return
meta_text = subcode_merge._merge_metadata(files, option)
positions = subcode_merge.load_potisions(mode, config)
if extract == False:
titles = subcode_merge._merge_title(files, mode, option, config)
else:
titles = []
for key in positions["must"]:
titles.append(positions["must"][key])
for key in positions["option"]:
titles.append(positions["option"][key])
# update positions to merged title
if ("id" in positions["option"]) == False:
positions["option"]["id"] = "id"
if (positions["option"]["id"] in titles) == False:
titles.insert(0, positions["option"]["id"])
if ("func" in positions["option"]) == False:
positions["option"]["func"] = "func"
if ("exonic_func" in positions["option"]) == False:
positions["option"]["exonic_func"] = "exonic_func"
if ("merge_func" in positions["option"]) == False:
positions["option"]["merge_func"] = "merge_func"
if (positions["option"]["merge_func"] in titles) == False \
and positions["option"]["func"] in titles \
and positions["option"]["exonic_func"] in titles:
pos = titles.index(positions["option"]["func"])
if pos < titles.index(positions["option"]["exonic_func"]):
pos = titles.index(positions["option"]["exonic_func"])
titles.insert(pos+1, positions["option"]["merge_func"])
[rep1, rep2] = subcode_merge._split_char(mode, config)
# write meta-data to file
f = open(output_file + ".tmp", mode = "w")
f.write(meta_text)
f.write(option["sept_out"].join(titles))
f.write("\n")
for idx in range(len(files)):
file_path = files[idx]
header = []
mapper = []
lines = []
lines_count = 0
for line in open(file_path):
line = line.rstrip()
if len(line.replace(option["sept"], "")) == 0:
continue
if len(option["comment"]) > 0 and line.find(option["comment"]) == 0:
continue
line = line.replace(rep1, rep2)
if len(header) == 0:
header = line.split(option["sept"])
mapper = calc_map(header, titles)
continue
data = line.split(option["sept"])
sort_data = []
func = ""
exonic = ""
for i in range(len(titles)):
if mapper[i] < 0:
# add columuns
if titles[i] == positions["option"]["id"]:
sort_data.append(ids[idx])
elif titles[i] == positions["option"]["merge_func"]:
if func.find("splicing") >= 0:
sort_data.append("splicing")
else:
sort_data.append(exonic)
else:
sort_data.append(option["lack"])
else:
if titles[i] == positions["option"]["func"]:
func = data[mapper[i]]
elif titles[i] == positions["option"]["exonic_func"]:
exonic = data[mapper[i]]
sort_data.append(data[mapper[i]])
lines.append(option["sept_out"].join(sort_data) + "\n")
lines_count += 1
if (lines_count > 10000):
f.writelines(lines)
lines = []
lines_count = 0
if (lines_count > 0):
f.writelines(lines)
f.close()
os.rename(output_file + ".tmp", output_file)
