def main():
draw_me = False
sum_only = False
MHC = False
regions = pc_toolbox.create_region_list(REGION_LOC)
bfile = BFILE
#ldfolder = LDFOLDER
ldfolder = '/home/jkb4y/ubs/work/results/Intersection_06022014/eurmeta_LD/'
#outfolder = OUTFOLDER
outfolder = '/home/jkb4y/ubs/work/results/Intersection_06022014/CAnalysis_LD/'
assoc_folder = ASSOC_FOLDER
#assoc_folder = '/home/jkb4y/work/results/Intersection_06022014/CAnalysis_eurmeta'
#for r2 in ['0','0.2','0.4','0.6','0.8']:
for r2 in ['0']:
#for r2 in ['0','0.2']:
#for r2 in ['0.2','0.4']:
#for r2 in ['0.8','0.6']:
#r2 = '0.8'
tot_loc = os.path.join(ldfolder,'all_regions_r2_{0}.ld'.format(r2))
with open(tot_loc, mode="w") as total:
ld_title_list = ['CHR_A','BP_A','SNP_A','CHR_B','BP_B','SNP_B','R2']
total.write('\t'.join(ld_title_list)+'\n')
for region in regions:
chrband = region.ID
chromosome = region.chro
subfolder = pc_toolbox.chr_folder(outfolder, chromosome)
assoc_chr_folder = pc_toolbox.chr_folder(assoc_folder, chromosome)
if chrband == '6p21.32' and not MHC:
continue
ld, snp_loc = plink_ld(region, bfile, ldfolder, assoc_chr_folder, r2, sum_only)
copy_to_tot(tot_loc, ld)
lz_ld = ld_for_lz(ld)
main_lz(region, subfolder, assoc_chr_folder, snp_loc,lz_ld, r2, draw_me)
def main():
regions = pc_toolbox.create_region_list(REGION_LOC)
ldfolder = '/home/jkb4y/work/results/2012Feb1/hg18/LD/'
outfolder = '/home/jkb4y/work/results/2012Feb1/hg18/CAnalysis_Test/'
for region in regions:
chrband = region.band
chromosome = region.chro
subfolder = pc_toolbox.chr_folder(outfolder, chromosome)
ldfile = chrband + '_r2_0.8_lz.ld'
ld_sub = pc_toolbox.chr_folder(ldfolder, chromosome)
ld = os.path.join(ld_sub,ldfile)
snp_list = '{0}_~leastP_SNPs.txt'.format(chrband)
snp_loc = os.path.join(ld_sub,snp_list)
main_lz(region, subfolder, snp_loc,ld)
def plink_ld(region, bfile, ldfolder, assoc_folder, r2, sum_only=False):
chromosome = region.chro
chrband = region.ID
ldfile = chrband + '_r2_{0}'.format(r2)
#ldfile = 'EVI5_EXPERIMENT_r2_{0}'.format(r2)
ld_sub = pc_toolbox.chr_folder(ldfolder, chromosome)
ld = os.path.join(ld_sub,ldfile)
#snp_list = 'EVI5_EXPERIMENT.txt'
snp_list = '{0}_~leastP_SNPs.txt'.format(chrband)
snp_loc = os.path.join(assoc_folder,snp_list)
if sum_only:
return ld + '.ld', snp_loc
plink_args = ['plink','--noweb','--bfile',bfile, '--chr', chromosome,
'--from-mb', region.start, '--to-mb',region.end,
'--r2','--ld-window-r2',r2,'--ld-window','999999',
'--ld-window-kb','99999','--ld-snp-list',snp_loc,
'--out', ld,'--filter-controls','--maf', '0.005']
p = subprocess.Popen(plink_args, bufsize = 0, executable=None,stdin=None,
stdout=None,stderr=None, preexec_fn=None,close_fds=False,
shell=False,cwd=None,env=None, universal_newlines=False,
startupinfo=None, creationflags=0)
p.wait()
return ld + '.ld', snp_loc
def main(argv):
global loopcount, output_folder, plink_test, chromosome, refgene
global maxloops, loopagain, SNP_loc, range_start_bp, range_end_bp
global out_flag, condition_list, firstloop, pheno_tag, c_interval
global chrband, interrupt
firstloop = True
loopagain = True
loopcount = 0
cl_arguments(argv)
label = ""
mb_start = convert_bp_to_mb(range_start_bp)
mb_end = convert_bp_to_mb(range_end_bp)
cl_indicator = ""
rgene = refgene
cband = chrband
ptag = ""
if not pheno_tag == "":
ptag = "_" + pheno_tag
if chrband is None:
rangelabel = range_label(chromosome, refgene, range_start_bp, range_end_bp)
cband = "NA"
else:
rangelabel = chrband
if condition_list is not None:
if interrupt:
if "~" in condition_list:
cl_indicator = "~"
else:
cl_indicator = "~"
if refgene is None:
rgene = "NA"
label = rangelabel.replace(":", "_") + ptag + out_flag + "_" + cl_indicator
of = "--"
if not out_flag == "":
of_pretty_list = out_flag.split("_")
of = of_pretty_list[1]
sys.stdout.write(
"""
******************************************************************************
***********************************************************
Beginning pc_workhorse.py on {0} at
{1}
$$$ {2} {3} {4} {5} {6} {7}
***********************************************************
******************************************************************************
""".format(
label, time.strftime("%a,%c"), cband, chromosome, rgene, mb_start, mb_end, of + ptag
)
)
sys.stdout.flush()
output_folder = str(pc_toolbox.chr_folder(output_folder, chromosome))
os.chdir(output_folder)
assoc_extension = determine_extension(plink_test)
SNP_loc = os.path.join(output_folder, label + "leastP_SNPs.txt")
## if condition_list is not None:
## ref_snp = given_condition_list(SNP_loc, condition_list)
while loopcount < maxloops and loopagain == True:
print_snp_list(SNP_loc)
# ref_snp = None
if interrupt:
ref_snp, part_counter = given_condition_list(SNP_loc, condition_list, interrupt)
print (
"""
******************************************************
<<<PROCESS INTERRUPTED AFTER IDENTIFYING CONDITIONAL SNP: {0}>>>
PROCESS RESTARTED and LOGFILE APPENDED TO.
******************************************************
""".format(
loopcount
)
)
print loopcount
interrupt = False
assoc_file_basename = label + str(loopcount) + "_SNPsOut"
print assoc_file_basename
assoc_file_name = assoc_file_basename + assoc_extension
script_name = label + "script_" + str(loopcount) + ".txt"
write_script(assoc_file_basename, script_name)
plink(script_name)
if loopcount == 0 and condition_list is not None:
ref_snp, part_counter = given_condition_list(SNP_loc, condition_list, interrupt)
title = (
make_lz_title(rangelabel, pheno_tag, assoc_file_basename, ref_snp)
.replace("_z", "")
.replace("_a", "")
.replace("_b", "")
)
pdf_loc = locuszoom(
assoc_file_name, chromosome, range_start_bp, range_end_bp, assoc_file_basename, title, ref_snp
)
fix_pdf(pdf_loc)
ref_snp = None
loopcount = part_counter
else:
find_and_record(assoc_file_name, SNP_loc, condition_list, plink_test, c_interval)
sys.stdout.flush()
title = make_lz_title(rangelabel, pheno_tag, assoc_file_basename)
pdf_loc = locuszoom(assoc_file_name, chromosome, range_start_bp, range_end_bp, assoc_file_basename, title)
fix_pdf(pdf_loc)
loopcount = loopcount + 1
print (
"""
*****************************************************************
****************************************************
Termination condition reached, and pc_workhorse
ended at {0} for region {1} at {2}.
****************************************************
******************************************************************
""".format(
time.strftime("%a,%c"), cband, rangelabel
)
)
