def store_line(line, table_indices, assoc, annot_dict):
## print('Now storing info.')
if assoc:
line_info = pc_toolbox.assoc_tuple(line, table_indices)
else:
line_info = meta_toolbox.meta_tuple(line, table_indices,annot_dict)
return line_info
def filter_result(result_file, snpstar):
line1 = True
with open(result_file, mode="r") as result:
for line in result:
if line1:
index_dict = pc_toolbox.read_assoc_titles(line,
.95, 'logistic')
line1 = False
else:
lsplit = line.strip().split()
if lsplit[index_dict['snp']] == snpstar:
#print('$$$ '+ line.strip())
info_tuple = pc_toolbox.assoc_tuple(line, index_dict)
#print info_tuple
return info_tuple
def read_assoc(assoc_loc, SNP_loc,c_interval,plink_test, exp):
global p_bound, index_dict, firstloop
tuple_list = []
with open(assoc_loc, mode = 'r') as assoc_file:
line1_check = True
for assoc_line in assoc_file: #open the assoc file to be read
## assoc_list = assoc_line.split()
if line1_check:
if firstloop:
index_dict = pc_toolbox.read_assoc_titles(assoc_line, c_interval, plink_test)
## index_dict = identify_cols(assoc_list, c_interval, plink_test)
firstloop = False
if loopcount == 0:
if os.path.exists(SNP_loc):
clear = open(SNP_loc, mode='w')
clear.close()
line1_check = False
else:
tuplet = pc_toolbox.assoc_tuple(assoc_line, index_dict)
## tuplet = get_tuple(assoc_list, index_dict)
if is_number(tuplet.p) and tuplet.p < float(p_bound)* math.pow(10,exp):
tuple_list.append(tuplet)
return tuple_list
