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
