def read_assoc(assoc_loc, gene_name,gene_region_dict):
line1 = True
old_p = 1
old_out=[]
reg_chr, reg_start, reg_end = gene_region_dict[gene_name]
assoc_counter = 0
multi_counter = 1
sig_list = []
blank_dict = {'chr':'--','start':'--','end':'--','sym':'--','snp':'--',
'lz':'--','pval':'--','stat':'--','OR':'NA','aa1':'NA',
'pos':'--','notes':'--','maf':'NA','ma1':'NA','ma2':'NA'}
order_list = ['chr','start','end','sym','snp','lz','pval','stat','OR',
'aa1','maf','ma1','ma2','notes']
with open(assoc_loc, mode="r") as assoc:
for line in assoc:
line_list = line.strip().split()
if line1:
assoc_i = pc_toolbox.read_assoc_titles(line, c_interval)
## assoc_indices = read_assoc_titles(line)
assoc_counter = 1
line1 = False
else:
snp_pos = int(line_list[assoc_i['pos']])
if not line_list[assoc_i['p']] == 'NA':
if reg_chr == int(line_list[assoc_i['chr']]
) and pc_toolbox.in_interval(snp_pos,reg_start, reg_end):
cur_p = float(line_list[assoc_i['p']])
cur_snp , lz_snp = pc_toolbox.correct_snp(assoc_i,line_list)
## cur_snp = line_list[assoc_indices['snp']]
## lz_snp = '--'
## if not cur_snp.startswith('rs'):
## lz_snp = 'chr'+str(reg_chr)+':'+ str(snp_pos)
## else:
## lz_snp = cur_snp
cur_out = [str(reg_chr), str(reg_start), str(reg_end),gene_name,
cur_snp,lz_snp, str(cur_p), str(snp_pos),'--']
if cur_p == old_p:
multi_counter = multi_counter + 1
cur_tup = (cur_snp, lz_snp,str(cur_p))
old_tup = (old_out[4], old_out[5],str(old_p))
sig_list.append(cur_tup)
if old_tup not in sig_list:
sig_list.append(old_tup)
print('NOTE: Both {0} and {1} have p-values of {2}.'.format(old_out[4],cur_snp, cur_p))
print('There are no Z-scores with which to decide between them, so I arbitrarily retain {0}.'.format(old_out[4]))
old_out[8]='{0}SNPs(p={1})'.format(multi_counter, old_p)
print(old_out[8])
elif cur_p < old_p:
multi_counter = 1
old_p = cur_p
old_out = cur_out
sig_list = []
assoc_counter = assoc_counter + 1
return old_out, sig_list
def create_index_dict(table_loc, table_type):
line1 = True
with open(table_loc, mode = "r") as table:
for line in table:
if line1:
line1 = False
if table_type == 'family':
index_dict = pc_toolbox.read_fam_titles(line)
elif table_type == 'assoc':
index_dict = pc_toolbox.read_assoc_titles(line, c_interval=None,plink_test='logistic')
else:
index_dict = pc_toolbox.read_meta_titles(line)
return index_dict
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 edit_table(table_loc, table_type):
global perm
line1 = True
ztup_list = list()
## lz_table_loc = new_table_loc(table_loc)
with open(table_loc, mode="r") as table:
for line in table:
line_split = line.strip().split()
if line1:
if table_type == "assoc":
index_dict = pc_toolbox.read_assoc_titles(line, c_interval=None, plink_test="logistic")
elif table_type == "eqtl":
index_dict = achilleas_yank.read_eqtl_titles(line, perm)
print index_dict
else:
index_dict = pc_toolbox.read_meta_titles(line)
print index_dict
line1 = False
else:
## if line1:
## table_title_list = line_split
## parse_col()
## new_table.write('\t'.join(line_split)+'\n')
## line1 = False
## else:
## cur_chr = line_split[meta_chrcol]
cur_chr = line_split[index_dict["chr"]]
cur_pos = int(line_split[index_dict["pos"]])
## if not line_split[index_dict['snp']].startswith('rs'):
## line_split[index_dict['snp']]='chr'+cur_chr+':'+str(cur_pos)
if not line_split[index_dict["p"]] == "NA":
if float(line_split[index_dict["p"]]) == 0:
ZTup = namedtuple("ZTup", "lz,chro,pos,abs_z")
if assoc:
z_or_t = abs(float(line_split[index_dict["t"]]))
else:
z_or_t = abs(float(line_split[index_dict["z"]]))
z = ZTup(
lz=line_split[index_dict["snp"]],
chro=line_split[index_dict["chr"]],
pos=line_split[index_dict["pos"]],
abs_z=z_or_t,
)
ztup_list.append(z)
ztup_sort = sorted(ztup_list, key=lambda z: z.abs_z, reverse=True)
return index_dict, ztup_sort, table_loc
def make_snp_pos_list(input_assoc, output_name):
snplist = list()
line1 = True
with open(input_assoc, mode="r") as assoc:
for aline in assoc:
if line1:
index_dict = pc_toolbox.read_assoc_titles(aline,
.95, 'logistic')
line1 = False
else:
lsplit = aline.strip().split()
snp_tuple = (lsplit[index_dict['snp']], lsplit[index_dict['pos']])
snplist.append(snp_tuple)
with open(output_name, mode="w") as output:
for snp in snplist:
output.write('\t'.join(snp)+'\n')
return snplist
def read_table(table_loc, region_list, assoc, annot_dict):
#print("Now entering read_table.")
line1 = True
standardizer = 1e6
snp_list = []
with open(table_loc, mode="r") as table:
for line in table:
if line1:
if assoc:
table_indices = pc_toolbox.read_assoc_titles(line, .95, 'logistic')
else:
table_indices = pc_toolbox.read_meta_titles(line)
line1=False
else:
line_list = line.strip().split()
snp_pos = int(line_list[table_indices['pos']])
chro = int(line_list[table_indices['chr']])
p_str = line_list[table_indices['p']]
#print line_list
p_ok = True
if not pc_toolbox.is_number(p_str):
p_ok = False
elif float(p_str)>P_BOUND:
p_ok=False
in_reg = False
for region in region_list:
reg_chr = int(region.chro)
reg_start = int(float(region.start) *standardizer)
reg_end = int(float(region.end) * standardizer)
## print("Now checking region:")
## print region
if reg_chr == chro and pc_toolbox.in_interval(snp_pos, reg_start, reg_end):
in_reg = True
if p_ok and not in_reg:
snp_info = store_line(line, table_indices, assoc,annot_dict)
snp_list.append(snp_info)
print snp_list
sys.stdout.flush()
tuple_list = sorted(snp_list, key=attrgetter('chro', 'p'))
#snp_list.sort(key= lambda info : info.chro)
print snp_list
print tuple_list
sys.stdout.flush()
return tuple_list
def edit_table(table_loc, fix):
line1=True
ztup_list = []
lz_table_loc = new_table_loc(table_loc)
with open(table_loc, mode = 'r') as table:
if fix:
lz_table = open(lz_table_loc, mode='w')
#with open(lz_table_loc, mode='w')as lz_table:
for line in table:
line_split = line.strip().split()
if line1:
if assoc:
index_dict = pc_toolbox.read_assoc_titles(line, c_interval=None,plink_test='logistic')
else:
index_dict = pc_toolbox.read_meta_titles(line)
line1=False
else:
## if line1:
## table_title_list = line_split
## parse_col()
## new_table.write('\t'.join(line_split)+'\n')
## line1 = False
## else:
## cur_chr = line_split[meta_chrcol]
cur_chr = line_split[index_dict['chr']]
cur_pos = int(line_split[index_dict['pos']])
if not line_split[index_dict['snp']].startswith('rs'):
line_split[index_dict['snp']]='chr'+cur_chr+':'+str(cur_pos)
if not line_split[index_dict['p']]=='NA':
if float(line_split[index_dict['p']])==0:
ZTup = namedtuple('ZTup','lz,chro,pos')
z = ZTup(lz=line_split[index_dict['snp']],
chro=line_split[index_dict['chr']],
pos=line_split[index_dict['pos']])
ztup_list.append(z)
if fix:
lz_table.write('\t'.join(line_split)+'\n')
if fix:
lz_table.close()
table_loc = lz_table_loc
return index_dict, ztup_list, table_loc
def read_table(table_loc, chromosome, index_dict):
#global high_pos, low_pos
low_pos = 5000000000
high_pos = 0
line1 = True
with open(table_loc, mode='r') as table:
for line in table:
line_split = line.strip().split()
if line1:
if assoc:
index_dict = pc_toolbox.read_assoc_titles(line, c_interval=None,plink_test='logistic')
else:
index_dict = pc_toolbox.read_meta_titles(line)
line1=False
else:
cur_chr = line_split[index_dict['chr']]
cur_pos = int(line_split[index_dict['pos']])
if chromosome==cur_chr and cur_pos < low_pos:
low_pos = cur_pos
if chromosome==cur_chr and cur_pos > high_pos:
high_pos = cur_pos
return (low_pos,high_pos)
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
'a1':a1_index,
old_p = 1
old_out={}
old_t = 0
reg_chr = gene.chro
reg_start = int(float(gene.start) *standardizer)
reg_end = int(float(gene.end) * standardizer)
sym = gene.sym
band = gene.band
assoc_counter = 0
multi_counter = 1
zero_list = []
with open(assoc_loc, mode="r") as assoc:
for line in meta:
if line1:
assoc_indices = pc_toolbox.read_assoc_titles(line)
assoc_counter = 1
line1 = False
old_out = {'chr':'','band':'','start':'',
'end':'','sym':'','snp':'',
'p':'1','pos':'', 'or':'0',
'hi':'0', 'lo':'0','a1':'--',
't':'0','note':'--','checkme':'0'}
else:
line_info = read_assoc(line,.95, 'logistic')
##
##
##
##
##NOTE NOTE NOTE THIS IS WHERE EDITING STOPPED!!!! RESUME CHANGES HERE!!!!!!!!!!!!!
##
