def identify_zerops(region_list, zero_list):
z_region_list = list()
for zero in zero_list:
# print('Current ZTup being considered:')
# print zero
for region in region_list:
## print('Current Region being considered:')
## print region
if str(zero.chro) == str(region.chro) and pc_toolbox.in_interval(
float(zero.pos), float(region.start), float(region.end)
):
if region not in z_region_list:
z_region_list.append(region)
print (
"""
***********************************************************
NOTE: REMOVING Region {0} from first list due to:
{1} at chr{2}:{3} with p=0.
***********************************************************
""".format(
region.ID, zero.lz, zero.chro, zero.pos
)
)
sys.stdout.flush()
continue
# region_list.remove(region)
sys.stdout.flush()
return region_list, z_region_list
def read_meta(meta_loc, region, outfolder,build, annot_dict=None):
line1 = True
standardizer = 1e6
reg_chr = region.chro
reg_start = int(float(region.start) *standardizer)
reg_end = int(float(region.end) * standardizer)
sym = region.sym
band = region.band
outfile = os.path.join(outfolder,band+'.tbl')
out = open(outfile, mode = "w")
title_list = ['imchip_name','rs_name','chr','{0}_pos'.format(build),'p-value','z-score','weight','a1','a2']
out.write('\t'.join(title_list)+'\n')
with open(meta_loc, mode="r") as meta:
for line in meta:
if line1:
meta_indices = pc_toolbox.read_meta_titles(line)
line1 = False
else:
line_list = line.strip().split()
snp_pos = int(line_list[meta_indices['pos']])
weight = line_list[meta_indices['weight']]
if int(reg_chr) == int(line_list[meta_indices['chr']]
) and pc_toolbox.in_interval(snp_pos, reg_start, reg_end):
if float(weight)>WEIGHT_MIN:
p_val = line_list[meta_indices['p']]
lz_snp = line_list[meta_indices['snp']]
z_score = line_list[meta_indices['z']]
a1 = line_list[meta_indices['a1']]
a2 = line_list[meta_indices['a2']]
snp_rs = annot_dict[lz_snp].rs
snp_im = annot_dict[lz_snp].name
out.write('\t'.join([snp_im,snp_rs,reg_chr,str(snp_pos),p_val,z_score,weight,a1,a2])+'\n')
out.close()
def snp_in_interval(region_tuple, line_list, index_dict):
reg_chr,reg_start,reg_end = region_tuple
snp_pos = int(line_list[index_dict['pos']])
if not int(reg_chr) == int(line_list[index_dict['chr']]):
return False
elif pc_toolbox.in_interval(snp_pos, reg_start, reg_end):
return True
else:
return False
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:
if line1:
assoc_indices = read_assoc_titles(line)
assoc_counter = 1
line1 = False
else:
line_list = line.strip().split()
snp_pos = int(line_list[assoc_indices['pos']])
if not line_list[assoc_indices['p']] == 'NA':
if reg_chr == int(line_list[assoc_indices['chr']]) and pc_toolbox.in_interval(snp_pos,
reg_start, reg_end):
cur_p = float(line_list[assoc_indices['p']])
cur_snp , lz_snp = pc_toolbox.correct_snp(assoc_indices,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 filter_by_region(region, file_in, file_out, index_dict):
line1 = True
with open(file_in, mode="r") as ifiley:
with open(file_out, mode="w") as ofiley:
for line in ifiley:
line_split = line.strip().split()
if line1:
ofiley.write('\t'.join(line_split)+'\n')
line1=False
else:
bp = line_split[index_dict['pos']]
chro = line_split[index_dict['chr']]
if int(region.chro) == int(chro) and pc_toolbox.in_interval(int(bp),region.start,region.end):
ofiley.write('\t'.join(line_split)+'\n')
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 remove_zerops(region_list,zero_list):
for zero in zero_list:
## print('Current ZTup being considered:')
## print zero
for region in region_list:
## print('Current region being considered:')
## print region
if float(zero.chro) == float(region.chro) and pc_toolbox.in_interval(float(zero.pos),
float(region.start),
float(region.end)):
print('''
***********************************************************
NOTE: REMOVING Region {0} from list due to:
{1} at chr{2}:{3} with p=0.
***********************************************************
'''.format(region.band,zero.lz,zero.chro,zero.pos))
sys.stdout.flush()
region_list.remove(region)
return region_list
def read_table(table_loc, gene, table_type, annot_dict=None):
global weight_min, sex_weight
## print("Weight Min is:")
## print weight_min
line1 = True
standardizer = 1e6
## if position_form == 'mb':
## standardizer = 1e6
## elif position_form == 'kb':
## standardizer = 1e3
old_p = 1
old_out={}
old_abs_z = 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
ID = gene.ID
table_counter = 0
multi_counter = 1
zero_list = []
low_w_p = 1
with open(table_loc, mode="r") as table:
for line in table:
if line1:
if table_type == 'META':
index_dict = pc_toolbox.read_meta_titles(line)
if table_type == 'FAMILY':
index_dict = pc_toolbox.read_fam_titles(line)
table_counter = 1
line1 = False
old_out = {'chr':'','ID':'','start':'',
'end':'','sym':'','snp':'','im':'',
'lz':'','p':'1','pos':'',
'|z|':'0','z':'0','note':'--',
'weight':'','maf':'','meta_a1':'',
'meta_a2':'', 'checkme':''}
lw_blank = {'chr':'','ID':'','start':'',
'end':'','sym':'','snp':None,'im':None,
'lz':None,'p':'1','pos':'',
'|z|':'0','z':'0','note':'--',
'weight':'','maf':'','meta_a1':'',
'meta_a2':''}
low_weight_out = lw_blank
#,'checkme':'0'}
else:
line_list = line.strip().split()
snp_pos = int(line_list[index_dict['pos']])
if int(reg_chr) == int(line_list[index_dict['chr']]
) and pc_toolbox.in_interval(snp_pos, reg_start, reg_end):
old_p = float(old_out['p'])
cur_p = float(line_list[index_dict['p']])
lz_snp = line_list[index_dict['snp']]
cur_w = float(line_list[index_dict['weight']])
cur_a1 = line_list[index_dict['a1']]
cur_a2 = line_list[index_dict['a2']]
cur_abs_z = abs(float(line_list[index_dict['z']]))
cur_z = line_list[index_dict['z']]
cur_snp = annot_dict[lz_snp].rs
cur_im = annot_dict[lz_snp].name
#snp, lz_snp = meta_toolbox.correct_snp(index_dict, line_list, annot_dict)
## if annot_dict is None:
## lz_snp=cur_snp
## if not cur_snp.startswith("rs"):
## lz_snp = 'chr'+str(reg_chr)+':'+ str(snp_pos)
## else:
## lz_snp = annot_dict[cur_snp].lz
## if not cur_snp.startswith('rs'):
## lz_snp = 'chr'+str(reg_chr)+':'+ str(snp_pos)
## else:
## lz_snp = cur_snp
cur_out = {'chr':gene.chro,'ID':gene.ID,'start':gene.start,
'end':gene.end,'sym':gene.sym,'snp':cur_snp,'im':cur_im,
'lz':lz_snp,'p':str(cur_p),'pos':str(snp_pos),
'|z|':str(cur_abs_z),'z':cur_z,'note':'--',
#'checkme':'0',
'weight':str(cur_w), 'meta_a1':cur_a1,'meta_a2':cur_a2}
if float(cur_out['weight']) < weight_min:
#print("Weight ({0}) is less than Minimum ({1}).".format(str(cur_w),weight_min))
cur_out['checkme']='1'
else:
cur_out['checkme']='0'
## if cur_w > weight_min or (reg_chr in ['23','24'] and cur_w > sex_weight):
## cur_out = {'chr':gene.chro,'band':gene.band,'start':gene.start,
## 'end':gene.end,'sym':gene.sym,'snp':cur_snp,
## 'lz':lz_snp,'p':str(cur_p),'pos':str(snp_pos),
## '|z|':str(cur_abs_z),'z':cur_z,'note':'--','checkme':'0',
## 'weight':str(cur_w), 'meta_a1':cur_a1,'meta_a2':cur_a2}
## else:
## cur_out = {'chr':gene.chro,'band':gene.band,'start':gene.start,
## 'end':gene.end,'sym':gene.sym,'snp':cur_snp,
## 'lz':lz_snp,'p':str(cur_p),'pos':str(snp_pos),
## '|z|':str(cur_abs_z),'z':cur_z,'note':'--','checkme':'1',
## 'weight':str(cur_w), 'meta_a1':cur_a1,'meta_a2':cur_a2}
if cur_p == old_p:
multi_counter = multi_counter + 1
ZTup = namedtuple('ZTup','snp,lz,p,z,w')
cur_tup = ZTup(snp=cur_out['snp'],lz=cur_out['lz'],
p=cur_out['p'],z=cur_out['|z|'],w=cur_out['weight'])
old_tup = ZTup(snp=old_out['snp'],lz=old_out['lz'],
p=old_out['p'],z=old_out['|z|'],w=old_out['weight'])
zero_list.append(cur_tup)
if old_tup not in zero_list:
zero_list.append(old_tup)
print('NOTE: Both {0} and {1} have p-values of {2}.'.format(old_out['snp'],cur_snp, cur_p))
print('{0} has a z-score of: {1}'.format(old_out['snp'],old_out['z']))
print('{0} has a z-score of: {1}'.format(cur_out['snp'],cur_out['z']))
if cur_out['|z|'] > old_out['|z|'] and cur_out['checkme']=='0':
old_p = cur_p
old_abs_z = cur_abs_z
old_out.update(cur_out)
print('Retaining {0} as the significant SNP based on z-score value.'.format(old_out['snp']))
old_out['note']='{0}SNPs(p={1})'.format(multi_counter, old_p)
elif cur_p < old_p:
if cur_out['checkme']=='0':
multi_counter = 1
old_p = cur_p
old_out.update(cur_out)
zero_list = []
if not low_weight_out['p'] == '1':
if cur_p < float(low_weight_out['p']):
low_weight_out = lw_blank
low_weight_out['p']='1'
low_weight_out['lz']=None
print("Wiping low weight snp!")
elif cur_p < float(low_weight_out['p']):
low_weight_out.update(cur_out)
print('''Adding {0} to low weight SNP list due to
weight = {1}
p-value = {2}'''.format(cur_snp, low_weight_out['weight'],low_weight_out['p']))
table_counter = table_counter + 1
sorted_list = sorted(zero_list, key=lambda member: member[3], reverse=True)
#print old_out
return old_out, sorted_list, low_weight_out['lz']
't':'0','note':'--','checkme':'0'}
else:
line_info = read_assoc(line,.95, 'logistic')
##
##
##
##
##NOTE NOTE NOTE THIS IS WHERE EDITING STOPPED!!!! RESUME CHANGES HERE!!!!!!!!!!!!!
##
##
##
##
line_list = line.strip().split()
snp_pos = int(line_list[assoc_indices['pos']])
if int(reg_chr) == int(line_list[assoc_indices['chr']]
) and pc_toolbox.in_interval(snp_pos, reg_start, reg_end):
old_p = float(old_out['p'])
cur_p = float(line_list[assoc_indices['p']])
cur_snp = line_list[assoc_indices['snp']]
cur_t = float(line_list[assoc_indices['t']])
cur_hi = line_list[assoc_indices['hi']]
cur_lo = line_list[assoc_indices['lo']]
cur_a1 = line_list[assoc_indices['a1']]
cur_or = line_list[assoc_indices['or']]
## if not cur_snp.startswith('rs'):
## lz_snp = 'chr'+str(reg_chr)+':'+ str(snp_pos)
## else:
## lz_snp = cur_snp
## if cur_w > weight_min or (reg_chr in ['23','24'] and cur_w > sex_weight):
## cur_out = {'chr':gene.chro,'band':gene.band,'start':gene.start,
