def make_ref_dict(yank_loc): ref_dict = dict() with open(yank_loc, mode="r") as yank: line1 = True for line in yank: line_list = line.strip().split() if line1: yank_indices = pc_toolbox.read_yank_titles(line) line1 = False else: ref_dict[line_list[yank_indices["id"]]] = (line_list[yank_indices["lz"]],line_list[yank_indices["im"]]) return ref_dict
def get_snp_list(meta_yank_loc): line1 = True snp_list = list() counter = 0 with open(meta_yank_loc, mode = "r") as meta: for line in meta: if line1: yank_indices = pc_toolbox.read_yank_titles(line) line1 = False else: line_list = line.strip().split() snp_list.append(line_list[yank_indices['lz']]) counter = counter + 1 print("I find {0} SNPs in the meta_yank list.".format(counter)) return snp_list
def read_yank(yank_loc): line1 = True with open(yank_loc, mode="r") as yank: yank_lines = list() for line in yank: if line1: index_dict = pc_toolbox.read_yank_titles(line) line1 = False else: lsplit = line.strip().split() if not lsplit == []: yank_info = YankInfo(start=lsplit[index_dict['start']], end=lsplit[index_dict['end']], chro=lsplit[index_dict['chr']], lz=lsplit[index_dict['lz']], ID=lsplit[index_dict['id']], pos=lsplit[index_dict['pos']], p=lsplit[index_dict['p']]) yank_lines.append(yank_info) return yank_lines