def __construct_tree_dict(in_file, in_id, merge_tree_dict):
in_fp = bp.FileParser(in_file)
for in_items in in_fp.iter():
in_fp.print_prog()
cur_chr = in_items[0][3:]
cur_pos = int(in_items[1])
cur_tag = in_items[-1]
if "V" in cur_tag:
type_tag = "pc_ind" if "ind" in cur_tag else "pc_snv"
elif "refhom" in cur_tag:
type_tag = "nc_low"
else:
type_tag = "nc_ind" if "ind" in cur_tag else "nc_snv"
af = round(float(in_items[5]), FLOAT_PREC)
cur_info = f"{in_id}_{'_'.join(in_items[2:5])}_{af}_{'_'.join(in_items[6:8])}"
if type_tag not in merge_tree_dict:
merge_tree_dict[type_tag] = dict()
if cur_chr not in merge_tree_dict[type_tag]:
merge_tree_dict[type_tag][cur_chr] = tree.RBTree()
prev_info = merge_tree_dict[type_tag][cur_chr].search(cur_pos)
if prev_info:
if prev_info.split(";")[0] != cur_tag:
print("WARNING: Inconsistent tag for locus")
cur_info = f"{prev_info};{cur_info}"
else:
cur_info = f"{cur_tag};{cur_info}"
merge_tree_dict[type_tag][cur_chr].insert(cur_pos, cur_info)
return
def construct_from_bed(in_file: str):
dict_tree = dict()
in_fp = bp.FileParser(in_file)
for in_items in in_fp.iter():
in_fp.print_prog()
cur_chr: str = in_items[0]
cur_start: int = int(in_items[1]) + 1
cur_end: int = int(in_items[2])
if cur_chr not in dict_tree:
dict_tree[cur_chr] = tree.RBITree()
q_res = dict_tree[cur_chr].search(cur_start)
if q_res:
print(f"WARNING: Overlap found: {cur_chr}:{cur_start} - {q_res}")
dict_tree[cur_chr].insert(cur_start, "0/0", cur_end)
in_fp.close()
return dict_tree
def construct_from_vcf(in_file: str):
dict_tree = dict()
in_fp = bp.FileParser(in_file)
for in_items in in_fp.iter():
in_fp.print_prog()
cur_chr: str = in_items[0]
cur_pos: int = int(in_items[1])
if cur_chr not in dict_tree:
dict_tree[cur_chr] = tree.RBITree()
q_res = dict_tree[cur_chr].search(cur_pos)
if q_res:
print(f"WARNING: Overlap found: {cur_chr}:{cur_pos} - {q_res}")
proc_res = process_vcf_line(in_items)
cur_info: str = "-".join(proc_res)
dict_tree[cur_chr].insert(cur_pos, cur_info)
in_fp.close()
return dict_tree
if ctrl_info not in tag_count_dict:
tag_count_dict[ctrl_info] = 0
tag_count_dict[ctrl_info] += 1
print(
f"{chrpos} | CurThres: {rep_test[1]:<6.3f} | Count: {rep_test[2]}")
else:
tag_count_dict["na"] += 1
print(f"{chrpos} | CurThres: ??? | Count: 0")
out_f.write(f"{chrpos[0]}\t{chrpos[1]}\t{HOLDER_STR}\n")
if __name__ == '__main__':
print(f"# Reference: {CTRL_FILE}")
print(f"# Input: {IN_FILE}")
print(f"# Reproducibility threshold: {threshold}")
ref_fp = bp.FileParser(CTRL_FILE)
in_fp = bp.FileParser(IN_FILE)
out_f = open(OUT_FILE, "w")
bp.write_vcf_hd(out_f)
tag_count_dict = {"na": 0}
for ref_items in ref_fp.iter():
if in_fp.term:
if not IGNORE_NULL:
__print_and_write(out_f, ref_items, tag_count_dict)
continue
cmp_res = bp.cmp_lines(ref_items, in_fp.get_line())
while cmp_res > 0:
in_fp.next()
if in_fp.term:
break
cmp_res = bp.cmp_lines(ref_items, in_fp.get_line())
for out_id in OUT_ID_TUP:
out_file = f"{OUT_DIR}/{IN_ID}.parse.{out_id}.txt"
print(out_file)
out_dict[out_id] = open(out_file, "w")
return out_dict
if __name__ == '__main__':
in_file_list = glob.glob(f"{IN_DIR}/*{IN_ID}.parse.txt")
if len(in_file_list) != 1:
print("ERROR: Invalid input file")
sys.exit()
else:
print(f"** Input: {in_file_list[0]}")
out_dict = __create_out_dict()
in_fp = bp.FileParser(in_file_list[0])
in_var_tup = SAMP_TO_VAR[IN_MOS] if IN_MOS in SAMP_TO_VAR else tuple()
for in_items in in_fp.iter():
in_fp.print_prog()
cur_id = in_items[-1]
if cur_id[0] == "[":
cur_id = cur_id[2:-2].split(";")[0]
if NAIVE:
out_l = "{}\t{}".format("\t".join(in_items[:-1]), cur_id)
else:
out_l = "{}\t{}\t{}".format("\t".join(in_items[:3]),
"\t".join(in_items[4:9]), cur_id)
if not no_refhom and "refhom" in cur_id:
out_dict["nc_low"].write(f"{out_l}\n")
elif cur_id.split("_")[0] in in_var_tup:
if "ind" in cur_id:
IN_DIR = sys.argv[1]
IN_ID = sys.argv[2]
OUT_FILE = sys.argv[3]
def __grab_all_input(in_dir, in_id):
in_wc = in_id if "*" in in_id else f"{in_id}*"
return glob.glob(f"{in_dir}/{in_wc}")
if __name__ == '__main__':
in_file_list = __grab_all_input(IN_DIR, IN_ID)
print(f"# Inputs: {len(in_file_list)}")
for in_file in in_file_list:
print(in_file)
out_f = open(OUT_FILE, "w")
bp.write_vcf_hd(out_f)
for chr_num in bp.iter_chrom():
cur_file = None
for in_file in in_file_list:
if f".chr{chr_num}." in in_file:
cur_file = in_file
break
if not cur_file:
continue
cur_fp = bp.FileParser(cur_file)
for cur_item in cur_fp.iter():
out_f.write(f"{cur_fp.get_line().strip()}\n")
cur_fp.close()
out_f.close()
if in_items[6] != "PASS":
return False
cur_gt = __convert_gt(in_items[-1].split(":")[0])
if not cur_gt or cur_gt not in VALID_GT_SET:
return False
alt_base_list = in_items[4].split(",")
if "<*>" in alt_base_list:
alt_base_list.remove("<*>")
if len(alt_base_list) > 1:
return False
return True
if __name__ == '__main__':
print(f"# Input: {IN_FILE}")
in_fp = bp.FileParser(IN_FILE)
pass_f = open(PASS_FILE, "w")
fail_f = open(FAIL_FILE, "w")
bp.write_vcf_hd(pass_f)
bp.write_vcf_hd(fail_f)
prev_chrpos: str = "chr1.0"
for in_items in in_fp.iter():
in_fp.print_prog()
in_l = in_fp.get_line().rstrip()
cur_chrpos: str = f"{in_items[0]}.{in_items[1]}")
if cur_chrpos == prev_chrpos:
print(f"WARNING: Multiallelic site: {in_l}")
fail_f.write(f"{in_l}\n")
elif __validate_line(in_items):
pass_f.write(f"{in_l}\n")
else:
return None
out_list = ref_items[:2]
var_id = ref_gt
var_id += "_ind" if len(ref_items[3]) != len(ref_items[4]) else "_snv"
out_list.append(var_id)
out_list += ref_items[3:5]
return "{}\t{}\n".format("\t".join(out_list), HOLDER_STR)
elif sk_items[2] == in_items[2]:
return "{}\n".format("\t".join(ref_items))
return None
if __name__ == '__main__':
print(f"# SK Input: {SK_FILE}")
print(f"# DV Input: {DV_FILE}")
sk_fp = bp.FileParser(SK_FILE)
dv_fp = bp.FileParser(DV_FILE)
out_f = open(OUT_FILE, "w")
bp.write_vcf_hd(out_f)
for sk_items in sk_fp.iter():
if dv_fp.term:
break
cmp_res = bp.cmp_lines(sk_items, dv_fp.get_items())
while cmp_res > 0:
dv_fp.next()
if dv_fp.term:
break
cmp_res = bp.cmp_lines(sk_items, dv_fp.get_items())
if dv_fp.term:
break
elif cmp_res == 0:
