def find_leastP_SNPs(gene_region_list, table_loc, out_base, freq_loc, keep_loc, table_type, annot_dict):
title_list = TITLE_LIST
zero_title_list = ['snp_name','locuszoom_snp','p-value','|z-score|','weight']
title_line = '\t'.join(title_list)
zero_line = '\t'.join(zero_title_list)
keep = open(keep_loc,mode="w")
z_list = list()
lw_list = list()
out_file = out_base + '_yank.tbl'
with open(out_file, mode="w") as out_text:
out_text.write(title_line +'\n')
with open(out_file, mode="a") as out_text:
for gene in gene_region_list:
gene_info, zero_list, lw_snp = read_table(table_loc, gene, table_type, annot_dict)#, position_form)
keep.write(gene_info['lz']+'\n')
if not zero_list == []:
#zero_start, ext = os.path.splitext(out_file)
zero_path = out_base + '_yank_'+gene_info['ID'] +'.txt'
zeros = open(zero_path,mode='w')
zeros.write(zero_line +'\n')
for zero in zero_list:
zeros.write('\t'.join(zero)+'\n')
zeros.close()
freq_info = pc_toolbox.retrieve_freq(freq_loc, gene_info['snp'])
if freq_info == None:
freq_info = pc_toolbox.retrieve_freq(freq_loc, gene_info['lz'])
if freq_info == None:
gene_info.update({'maf':'NA','control_a1':'NA',
'control_a2':'NA'})
else:
gene_info.update({'maf':freq_info[0],'control_a1':freq_info[1],
'control_a2':freq_info[2]})
for item in ORDER_LIST:
print gene_info
out_text.write(str(gene_info[item]) + '\t')
out_text.write('\n')
if lw_snp is not None:
lw_list.append(lw_snp)
z_list = create_condition_list(gene_info, table_loc, out_file, z_list)
keep.close()
print z_list
print lw_list
return z_list, lw_list
def update_with_freq(freq_loc, snp_info, pop, aa_freq_loc=None):
print snp_info
print ("3")
if pop == 'UK' and aa_freq_loc == None:
if snp_info['snp'] == 'NA':
snp_info.update({'maf':'NA','control_a1':'NA','control_a2':'NA'})
return snp_info
freq_info = pc_toolbox.retrieve_freq(freq_loc, snp_info['snp'])
if freq_info == None:
freq_info = pc_toolbox.retrieve_freq(freq_loc, snp_info['lz'])
if freq_info == None:
snp_info.update({'maf':'NA','control_a1':'NA','control_a2':'NA'})
else:
snp_info.update({'maf':freq_info[0],'control_a1':freq_info[1],
'control_a2':freq_info[2]})
return snp_info
else:
snp_info = update_with_aa_freq(aa_freq_loc, freq_loc, snp_info)
return snp_info
def update_with_aa_freq(aa_freq_loc,uk_freq_loc, snp_info):
print snp_info
print ("3")
if snp_info['snp'] == 'NA':
snp_info.update({'AA_maf':'NA','AA_control_a1':'NA','AA_control_a2':'NA'})
return snp_info
aa_freq_info = pc_toolbox.retrieve_freq(aa_freq_loc, snp_info['snp'])
if aa_freq_info == None:
aa_freq_info = pc_toolbox.retrieve_freq(aa_freq_loc, snp_info['lz'])
if aa_freq_info == None:
snp_info.update({'AA_maf':'NA','AA_control_a1':'NA','AA_control_a2':'NA'})
else:
snp_info.update({'AA_maf':aa_freq_info[0],'AA_control_a1':aa_freq_info[1],
'AA_control_a2':aa_freq_info[2]})
uk_freq_info = pc_toolbox.retrieve_freq(uk_freq_loc, snp_info['snp'])
if uk_freq_info == None:
uk_freq_info = pc_toolbox.retrieve_freq(uk_freq_loc, snp_info['lz'])
if uk_freq_info == None:
snp_info.update({'UK_maf':'NA','UK_control_a1':'NA','UK_control_a2':'NA'})
else:
snp_info.update({'UK_maf':uk_freq_info[0],'UK_control_a1':uk_freq_info[1],
'UK_control_a2':uk_freq_info[2]})
print snp_info
return snp_info
def read_log(log_summary,log_file,freq_loc,map_loc, repair_loc,annot_dict):
'''
Extract relevant information from log file and append it to a summary file.
Args:
log_file -- path to log file which has been formated in a specific manner
log_summary -- path to which summary information should be written
Returns:
Nothing.
'''
#values used to reinitialize non-range information in output_list
BLANK = '--'
empty_list = []
condition_list = empty_list
reset_val = [empty_list,BLANK,BLANK,BLANK,BLANK,BLANK,BLANK,BLANK,BLANK,BLANK,'--']
blank_dict = {'chr':'chr','band':'band','ref':'refgene','start':'start','end':'end','flag':'--',
'clist':BLANK,'im':BLANK,'sig':BLANK,'pval':BLANK, 'OR':BLANK,'lo':BLANK,
'hi':BLANK,'t':BLANK,'aa1':BLANK,'maf':BLANK,'ma1':BLANK,'ma2':BLANK,
'lz':BLANK,'ca':BLANK,'total':'--'}
order_list = ['chr','band','ref','start','end','flag','clist','im','sig','pval','OR','lo',
'hi','t','aa1','maf','ma1','ma2','lz','ca','total']
reset_list = ['clist','im','sig','pval','OR','lo',
'hi','t','aa1','maf','ma1','ma2','lz','ca']
output_dict = blank_dict
with open(log_file, mode='r')as log:
with open(log_summary, mode='a')as summary:
for logline in log:
#if logline begins '$$$', it contains the range info
if logline.startswith('$$$'):
range_info = mb_range(logline)
output_dict['band']=range_info.band
output_dict['chr']=range_info.chro
output_dict['ref']=range_info.gene
output_dict['start']=range_info.start
output_dict['end']=range_info.end
output_dict['flag']=range_info.flag
#if logline begins '%%%', info pertains to loop through plink_association.py
if logline.startswith('%%%'):
#if there is unprinted (and thus unwiped) loop information
#in output_dict, LocusZoom did not spit out
#a 'Found: ' phrase with reference SNP name. This is bad news!
if not output_dict['sig']==BLANK:
output_dict['lz'] = 'ERROR'
print('ERROR: LZ did not announce a reference SNP!')
print output_dict
dict_list = []
for key in order_list:
dict_list.append(output_dict[key])
print dict_list
summary.write('\t'.join(dict_list)+'\n')
#gather info pertaining to this loop through plink
snp_pv_loop = snp_p_loop(logline)
## print('SNP_PV_LOOP is: ')
## print snp_pv_loop
output_dict['sig']=snp_pv_loop[0]
output_dict['pval']=snp_pv_loop[1]
output_dict['ca']=snp_pv_loop[2]
#look up the allele frequency of the snp in the freq file
maf,ma1,ma2 = pc_toolbox.retrieve_freq(freq_loc, snp_pv_loop[0])
output_dict['maf']=maf
output_dict['ma1']=ma1
output_dict['ma2']=ma2
#look up the original Immunochip SNP name in the map file
#im = pc_toolbox.retrieve_im(map_loc, snp_pv_loop[0], repair_loc)
im = annot_dict[anp_pv_loop[0]].name
output_dict['im']=im
#if logline begins with Odds Ratio etc.
elif logline.startswith('Regression Coefficient') or logline.startswith('Odds Ratio'):
orbeta = logline.strip().partition(':')[2]
output_dict['OR']=orbeta
elif logline.startswith('Coefficient T-Statistic'):
stat = logline.strip().partition(':')[2]
output_dict['t']=stat
elif logline.startswith('A1:'):
aa1 = logline.strip().partition(':')[2]
output_dict['aa1']=aa1
#if logline begins 'Found: ', obtain name of LZ's reference SNP
elif logline.startswith('Found:'):
lz_snp = one_value(logline)
output_dict['lz']=lz_snp
if len(condition_list)==0:
output_dict['clist']=BLANK
else:
output_dict['clist']='['+','.join(condition_list)+']'
dict_list = []
for key in order_list:
dict_list.append(output_dict[key])
print dict_list
summary.write('\t'.join(dict_list)+'\n')
condition_list = []
#if output_dict['total'] is '--',
#then this is NOT last loop through plink_association.py.
#(if it were, p_a wouldn't give a ref SNP, and LZ would,
#leading to an expected mismatch.)
if output_dict['total']=='--':
if not output_dict['lz']==output_dict['sig']:
print('ERROR: plink_association and Locus Zoom did not identify the same reference SNP!')
summary.write('ERROR: PLINK_ASSOCIATION AND LOCUS ZOOM IDENTIFIED DIFFERENT REFERENCE SNPs! \n')
output_dict['total']='--'
for key in reset_list:
output_dict[key]=BLANK
#if logline begins ':::', this is final loop through p_a
elif logline.startswith(':::'):
final_loopcount = one_value(logline)
output_dict['total']=final_loopcount
output_dict['ca']=final_loopcount
#if logline begins '&&&', it contains a snp in condition list
elif logline.startswith('&&&'):
condition_list.append(one_value(logline))
print(condition_list)
elif logline.startswith('Confidence Interval'):
want = logline.partition(':')[2].strip()
lo = want.partition('-')[0].strip()
hi = want.partition('-')[2].strip()
output_dict['lo']=lo
output_dict['hi']=hi
next
def main(argv):
global outfolder, assoc, chromosome,snpstar
global out_flag, user_script_loc
global range_start_bp, range_end_bp, hit_index, hitstring
global region_id, build, single, ldfolder, freq_loc, multi, hit1
cl_arguments(argv)
placeholder = ''
annot_dict_loc = fix_it.locate_annot_dict(build)
annot_dict = fix_it.build_annot_dict('LOG',annot_dict_loc)
snpstar_im = annot_dict[snpstar].name
table_folder = os.path.join(outfolder, 'ResultTables')
summary_folder = os.path.join(outfolder, 'SummaryTables')
str_hit_index = str(hit_index)
if hit_index < 10:
str_hit_index = '0'+str_hit_index
if not os.path.exists(table_folder):
os.makedirs(table_folder)
if not os.path.exists(summary_folder):
os.makedirs(summary_folder)
chr_folder = os.path.join(outfolder, 'chr{0}'.format(chromosome))
if not os.path.exists(chr_folder):
os.makedirs(chr_folder)
reg_folder = os.path.join(chr_folder, region_id)
if multi:
placeholder = '_'+snpstar+'_'+str_hit_index
if not os.path.exists(reg_folder):
os.makedirs(reg_folder)
super_outbase = os.path.join(reg_folder, region_id)
list_loc = super_outbase + '_snps.list'
table_loc = os.path.join(chr_folder, region_id+placeholder+'.tbl')
new_table_loc = os.path.join(table_folder, region_id+placeholder+'.tbl')
summary_table_loc = os.path.join(summary_folder, region_id+placeholder+'.tbl')
print(table_loc)
snplist = make_snp_pos_list(assoc,list_loc)
ld_loc = os.path.join(ldfolder,'chr{0}'.format(chromosome),
'{0}_r2_0.ld'.format(region_id))
table = open(table_loc, mode="w")
table.write('\t'.join(['SNP*','SNP*_pos','SNP*_im','conditional_snp',
'csnp_im','csnp_pos','SNP*_pvalue','OR','ci_lo','ci_hi',
'a1',"r2","csnp_freq","csnp_freq_a1"])+'\n')
table.close()
index = 1
for snp_tuple in snplist:
snp = snp_tuple[0]
snp_pos = snp_tuple[1]
snp_im = annot_dict[snp].name
corrected_snp = snp.replace(':','_')
outbase = super_outbase+'_'+corrected_snp
script_loc = outbase + '.script'
assoc_out = outbase +'.assoc.logistic'
if hit1:
write_script(outbase,script_loc, user_script_loc, snp, single, hitstring)
plink(script_loc)
print('''
**********************************************************************
************************************************************
The data will be conditioned on the following SNP:
%%% {0}
This is snp #{1} in a list of {2}.
******************************************************
**********************************************************************
'''.format(snp,index,len(snplist)))
## if snp == snpstar:
## write_script(outbase,script_loc, user_script_loc, snp, single, hitstring)
## plink(script_loc)
elif not multi:
write_script(outbase,script_loc, user_script_loc, snp, single, snpstar)
plink(script_loc)
print('''
**********************************************************************
************************************************************
The data will be conditioned on the following SNP:
%%% {0}
This is snp #{1} in a list of {2}.
******************************************************
**********************************************************************
'''.format(snp,index,len(snplist)))
info = filter_result(assoc_out,snpstar)
snp_freq = pc_toolbox.retrieve_freq(freq_loc, snp)
r2 = pc_toolbox.retrieve_r2(snpstar,snp,ld_loc)
if r2 is None:
r2 = "???"
index = index + 1
with open(table_loc, mode='a') as table:
table.write('\t'.join([snpstar,info.pos, snpstar_im,
snp,snp_im,snp_pos,str(info.p),
info.OR,info.lo,info.hi,
info.a1,r2,snp_freq[0],snp_freq[1]])+'\n')
shutil.copy(table_loc, new_table_loc)
summarize_table(new_table_loc, summary_table_loc, snpstar)
