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main_function_realdata_M23.py
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from subprocess import Popen
import numpy as np
import os
from sys import argv
from alleles_generator.real_file import AllelesReal
from summary_statistics import afs_stats_bitarray
def main():
"""This takes in 3 real PLINK .tped files.
PLINK .tped with CGI or 1000 genomes HapMap populations.
PLINK .tped snp array data made from same HapMap individuals with PLINK exclude.
PLINK .tped snp array data with populations of interest."""
test = argv[1]
if test == 'test':
dir_data = 'tests/test_data/'
elif test == 'real':
dir_data = 'real_data/'
naf_CGI = 18
neu_CGI = 18
nas_CGI = 8
nJ = 28
nM = 28
nWA = 38
nEA = 38
print 'naf_CGI ' + str(naf_CGI)
print 'neu_CGI ' + str(neu_CGI)
print 'nas_CGI ' + str(nas_CGI)
print 'nWA ' + str(nWA)
print 'nEA ' + str(nEA)
print 'nJ ' + str(nJ)
print 'nM ' + str(nM)
CGI_file = str(dir_data)+'YRI9.CEU9.CHB4.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes_snpsonly_maf0.005'
CGIarray_file = str(dir_data)+'YRI9.CEU9.CHB4.chr1.atDNA.biAllelicSNPnoDI.genotypes_hg18_Behar_HGDP_FtDNA'
array_file = str(dir_data)+'Behar_HGDP_FtDNA_Jews_MidEast_chr1_subset_21509'
print CGI_file
print CGIarray_file
print array_file
seq_real_CGI_file = AllelesReal(str(CGI_file)+'.tped')
seqAF_CGI_bits = seq_real_CGI_file.make_bitarray_seq(0, naf_CGI)
seqEu_CGI_bits = seq_real_CGI_file.make_bitarray_seq(naf_CGI, naf_CGI + neu_CGI)
seqAs_CGI_bits = seq_real_CGI_file.make_bitarray_seq(naf_CGI + neu_CGI, naf_CGI + neu_CGI + nas_CGI)
seq_real_CGIarray_file = AllelesReal(str(CGIarray_file)+'.tped')
seqAf_asc_bits = seq_real_CGIarray_file.make_bitarray_seq(0, naf_CGI)
seqEu_asc_bits = seq_real_CGIarray_file.make_bitarray_seq(naf_CGI, naf_CGI + neu_CGI)
seqAs_asc_bits = seq_real_CGIarray_file.make_bitarray_seq(naf_CGI + neu_CGI, naf_CGI + neu_CGI + nas_CGI)
seq_real_array_file = AllelesReal(str(array_file)+'.tped')
seqJ_asc_bits = seq_real_array_file.make_bitarray_seq(0, nJ)
seqM_asc_bits = seq_real_array_file.make_bitarray_seq(nJ, nJ + nM)
seqEA_asc_bits = seq_real_array_file.make_bitarray_seq(nJ + nM, nJ + nM + nEA)
seqWA_asc_bits = seq_real_array_file.make_bitarray_seq(nJ + nM + nEA, nJ + nM + nEA + nWA)
res = []
Af_res = []
Af_res.extend(afs_stats_bitarray.base_S_ss(seqAF_CGI_bits, naf_CGI))
pi_AfCGI = afs_stats_bitarray.Pi2(Af_res[3], naf_CGI)
Af_res.append(afs_stats_bitarray.Tajimas(pi_AfCGI, Af_res[0], naf_CGI))
del (Af_res[3])
res.extend(Af_res)
head = 'SegS_Af_CGI\tSing_Af_CGI\tDupl_Af_CGI\tTajD_Af_CGI\t'
Eu_res = []
Eu_res.extend(afs_stats_bitarray.base_S_ss(seqEu_CGI_bits, neu_CGI))
pi_EuCGI = afs_stats_bitarray.Pi2(Eu_res[3], neu_CGI)
Eu_res.append(afs_stats_bitarray.Tajimas(pi_EuCGI, Eu_res[0], neu_CGI))
del (Eu_res[3])
res.extend(Eu_res)
head = head + 'SegS_Eu_CGI\tSing_Eu_CGI\tDupl_Eu_CGI\tTajD_Eu_CGI\t'
As_res = []
As_res.extend(afs_stats_bitarray.base_S_ss(seqAs_CGI_bits, nas_CGI))
pi_AsCGI = afs_stats_bitarray.Pi2(As_res[3], nas_CGI)
As_res.append(afs_stats_bitarray.Tajimas(pi_AsCGI, As_res[0], nas_CGI))
del (As_res[3])
res.extend(As_res)
head = head + 'SegS_As_CGI\tSing_As_CGI\tDupl_As_CGI\tTajD_As_CGI\t'
##fst between populations
res.append(afs_stats_bitarray.FST2(seqAF_CGI_bits, pi_AfCGI, naf_CGI, seqEu_CGI_bits, pi_EuCGI, neu_CGI))
res.append(afs_stats_bitarray.FST2(seqAF_CGI_bits, pi_AfCGI, naf_CGI, seqAs_CGI_bits, pi_AsCGI, nas_CGI))
res.append(afs_stats_bitarray.FST2(seqEu_CGI_bits, pi_EuCGI, neu_CGI, seqAs_CGI_bits, pi_AsCGI, nas_CGI))
head = head + 'FST_AfEu_CGI\tFST_AfAs_CGI\tFST_EuAs_CGI\t'
########Use Germline to find IBD on pseduo array ped and map files
run_germline = int(argv[2])
filenameped = str(dir_data)+'Behar_HGDP_FtDNA_Jews_MidEast_YRI9.CEU9.CHB4.chr1.ped'
filenamemap = str(dir_data)+'Behar_HGDP_FtDNA_Jews_MidEast_YRI9.CEU9.CHB4.chr1.map'
filenameout = str(dir_data)+'Behar_HGDP_FtDNA_Jews_MidEast_YRI9.CEU9.CHB4.chr1'
print 'run germline? '+str(run_germline)
if (run_germline == 0):
print 'Running Germline on ' + str(filenameped) + ' ' + str(filenamemap)
print 'p ' + str(filenameped) + ' ' + str(filenamemap) + ' ' + str(filenameout) + ' "-bits 10"'
germline = Popen.wait(Popen('bash ./bin/phasing_pipeline/gline.sh ./bin/germline-1-5-1/germline ' + str(filenameped) + ' ' + str(filenamemap) + ' ' + str(filenameout) + ' "-bits 10"', shell=True))
print 'finished running germline'
########Get IBD stats from Germline output
if os.path.isfile(str(filenameout) + '.match'):
print 'reading Germline IBD output'
filegermline = open(str(filenameout) + '.match', 'r')
IBDlengths_eAeA = []
IBDlengths_wAwA = []
IBDlengths_JJ = []
IBDlengths_MM = []
IBDlengths_EE = []
IBDlengths_eAwA = []
IBDlengths_eAE = []
IBDlengths_wAE = []
IBDlengths_eAJ = []
IBDlengths_wAJ = []
IBDlengths_eAM = []
IBDlengths_wAM = []
IBDlengths_JM = []
IBDlengths_JE = []
IBDlengths_ME = []
for line in filegermline:
pop1 = line.split()[0]
pop2 = line.split()[2]
segment = float(line.split()[10])
pair = str(pop1) + '_' + str(pop2)
if pair == 'EA_EA':
IBDlengths_eAeA.append(segment)
if pair == 'WA_WA':
IBDlengths_wAwA.append(segment)
if pair == 'J_J':
IBDlengths_JJ.append(segment)
if pair == 'M_M':
IBDlengths_MM.append(segment)
if pair == 'E_E':
IBDlengths_EE.append(segment)
if pair == 'EA_WA' or pair == 'WA_EA':
IBDlengths_eAwA.append(segment)
if pair == 'EA_E' or pair == 'E_EA':
IBDlengths_eAE.append(segment)
if pair == 'WA_E' or pair == 'E_WA':
IBDlengths_wAE.append(segment)
if pair == 'EA_J' or pair == 'J_EA':
IBDlengths_eAJ.append(segment)
if pair == 'WA_J' or pair == 'J_WA':
IBDlengths_wAJ.append(segment)
if pair == 'EA_M' or pair == 'M_EA':
IBDlengths_eAM.append(segment)
if pair == 'WA_M' or pair == 'M_WA':
IBDlengths_wAM.append(segment)
if pair == 'J_M' or pair == 'M_J':
IBDlengths_JM.append(segment)
if pair == 'J_E' or pair == 'E_J':
IBDlengths_JE.append(segment)
if pair == 'M_E' or pair == 'E_M':
IBDlengths_ME.append(segment)
filegermline.close()
print 'calculating summary stats'
IBDlengths_mean = []
IBDlengths_median = []
IBDlengths_num = []
IBDlengths_var = []
IBDlengths_mean30 = []
IBDlengths_median30 = []
IBDlengths_num30 = []
IBDlengths_var30 = []
pairs = [IBDlengths_eAeA, IBDlengths_wAwA, IBDlengths_JJ, IBDlengths_MM, IBDlengths_EE, IBDlengths_eAwA,
IBDlengths_eAE, IBDlengths_wAE, IBDlengths_eAJ, IBDlengths_wAJ, IBDlengths_eAM, IBDlengths_wAM,
IBDlengths_JM, IBDlengths_JE, IBDlengths_ME]
for p in pairs:
IBDlengths_num.append(len(p))
if len(p) < 1:
p.append(0)
IBDlengths_mean.append(np.mean(p))
IBDlengths_median.append(np.median(p))
IBDlengths_var.append(np.var(p))
#### Get IBD greater than 30 Mb
IBDlengths30 = []
for l in p:
if l > 30:
IBDlengths30.append(l)
IBDlengths_num30.append(len(IBDlengths30))
if len(IBDlengths30) == 0:
IBDlengths30.append(0)
IBDlengths_mean30.append(np.mean(IBDlengths30))
IBDlengths_median30.append(np.median(IBDlengths30))
IBDlengths_var30.append(np.var(IBDlengths30))
res.extend(IBDlengths_mean)
head = head + 'IBD_mean_eAeA\tIBD_mean_wAwA\tIBD_mean_JJ\tIBD_mean_MM\tIBD_mean_EE\tIBD_mean_eAwA\tIBD_mean_eAE\tIBD_mean_wAE\tIBD_mean_eAJ\tIBD_mean_wAJ\tIBD_mean_eAM\tIBD_mean_wAM\tIBD_mean_JM\tIBD_mean_JE\tIBD_mean_ME\t'
res.extend(IBDlengths_median)
head = head + 'IBD_median_eAeA\tIBD_median_wAwA\tIBD_median_JJ\tIBD_median_MM\tIBD_median_EE\tIBD_median_eAwA\tIBD_median_eAE\tIBD_median_wAE\tIBD_median_eAJ\tIBD_median_wAJ\tIBD_median_eAM\tIBD_median_wAM\tIBD_median_JM\tIBD_median_JE\tIBD_median_ME\t'
res.extend(IBDlengths_num)
head = head + 'IBD_num_eAeA\tIBD_num_wAwA\tIBD_num_JJ\tIBD_num_MM\tIBD_num_EE\tIBD_num_eAwA\tIBD_num_eAE\tIBD_num_wAE\tIBD_num_eAJ\tIBD_num_wAJ\tIBD_num_eAM\tIBD_num_wAM\tIBD_num_JM\tIBD_num_JE\tIBD_num_ME\t'
res.extend(IBDlengths_var)
head = head + 'IBD_var_eAeA\tIBD_var_wAwA\tIBD_var_JJ\tIBD_var_MM\tIBD_var_EE\tIBD_var_eAwA\tIBD_var_eAE\tIBD_var_wAE\tIBD_var_eAJ\tIBD_var_wAJ\tIBD_var_eAM\tIBD_var_wAM\tIBD_var_JM\tIBD_var_JE\tIBD_var_ME\t'
res.extend(IBDlengths_mean30)
head = head + 'IBD30_mean_eAeA\tIBD30_mean_wAwA\tIBD30_mean_JJ\tIBD30_mean_MM\tIBD30_mean_EE\tIBD30_mean_eAwA\tIBD30_mean_eAE\tIBD30_mean_wAE\tIBD30_mean_eAJ\tIBD30_mean_wAJ\tIBD30_mean_eAM\tIBD30_mean_wAM\tIBD30_mean_JM\tIBD30_mean_JE\tIBD30_mean_ME\t'
res.extend(IBDlengths_median30)
head = head + 'IBD30_median_eAeA\tIBD30_median_wAwA\tIBD30_median_JJ\tIBD30_median_MM\tIBD30_median_EE\tIBD30_median_eAwA\tIBD30_median_eAE\tIBD30_median_wAE\tIBD30_median_eAJ\tIBD30_median_wAJ\tIBD30_median_eAM\tIBD30_median_wAM\tIBD30_median_JM\tIBD30_median_JE\tIBD30_median_ME\t'
res.extend(IBDlengths_num30)
head = head + 'IBD30_num_eAeA\tIBD30_num_wAwA\tIBD30_num_JJ\tIBD30_num_MM\tIBD30_num_EE\tIBD30_num_eAwA\tIBD30_num_eAE\tIBD30_num_wAE\tIBD30_num_eAJ\tIBD30_num_wAJ\tIBD30_num_eAM\tIBD30_num_wAM\tIBD30_num_JM\tIBD30_num_JE\tIBD30_num_ME\t'
res.extend(IBDlengths_var30)
head = head + 'IBD30_var_eAeA\tIBD30_var_wAwA\tIBD30_var_JJ\tIBD30_var_MM\tIBD30_var_EE\tIBD30_var_eAwA\tIBD30_var_eAE\tIBD30_var_wAE\tIBD30_var_eAJ\tIBD30_var_wAJ\tIBD30_var_eAM\tIBD30_var_wAM\tIBD30_var_JM\tIBD30_var_JE\tIBD30_var_ME\t'
Af_asc = []
ss_Af_asc = afs_stats_bitarray.base_S_ss(seqAf_asc_bits, naf_CGI)
if (ss_Af_asc[0] == 0):
for i in xrange(5):
Af_asc.append(0)
pi_Af_asc = 0
else:
Af_asc.extend(afs_stats_bitarray.base_S_ss(seqAf_asc_bits, naf_CGI))
pi_Af_asc = afs_stats_bitarray.Pi2(Af_asc[3], naf_CGI)
Af_asc.append(pi_Af_asc)
Af_asc.append(afs_stats_bitarray.Tajimas(pi_Af_asc, Af_asc[0], naf_CGI))
del (Af_asc[3])
res.extend(Af_asc)
head = head + 'SegS_Af_ASC\tSing_Af_ASC\tDupl_Af_ASC\tPi_Af_ASC\tTajD_Af_ASC\t'
Eu_asc = []
ss_Eu_asc = afs_stats_bitarray.base_S_ss(seqEu_asc_bits, neu_CGI)
if (ss_Eu_asc[0] == 0):
for i in xrange(5):
Eu_asc.append(0)
pi_Eu_asc = 0
else:
Eu_asc.extend(afs_stats_bitarray.base_S_ss(seqEu_asc_bits, neu_CGI))
pi_Eu_asc = afs_stats_bitarray.Pi2(Eu_asc[3], neu_CGI)
Eu_asc.append(pi_Eu_asc)
Eu_asc.append(afs_stats_bitarray.Tajimas(pi_Eu_asc, Eu_asc[0], neu_CGI))
del (Eu_asc[3])
res.extend(Eu_asc)
head = head + 'SegS_Eu_ASC\tSing_Eu_ASC\tDupl_Eu_ASC\tPi_Eu_ASC\tTajD_Eu_ASC\t'
As_asc = []
ss_As_asc = afs_stats_bitarray.base_S_ss(seqAs_asc_bits, nas_CGI)
if (ss_As_asc[0] == 0):
for i in xrange(5):
As_asc.append(0)
pi_As_asc = 0
else:
As_asc.extend(afs_stats_bitarray.base_S_ss(seqAs_asc_bits, nas_CGI))
pi_As_asc = afs_stats_bitarray.Pi2(As_asc[3], nas_CGI)
As_asc.append(pi_As_asc)
As_asc.append(afs_stats_bitarray.Tajimas(pi_As_asc, As_asc[0], nas_CGI))
del (As_asc[3])
res.extend(As_asc)
head = head + 'SegS_As_ASC\tSing_As_ASC\tDupl_As_ASC\tPi_As_ASC\tTajD_As_ASC\t'
J_asc = []
ss_J_asc = afs_stats_bitarray.base_S_ss(seqJ_asc_bits, nJ)
if (ss_J_asc[0] == 0):
for i in xrange(5):
J_asc.append(0)
pi_J_asc = 0
else:
J_asc.extend(afs_stats_bitarray.base_S_ss(seqJ_asc_bits, nJ))
pi_J_asc = afs_stats_bitarray.Pi2(J_asc[3], nJ)
J_asc.append(pi_J_asc)
J_asc.append(afs_stats_bitarray.Tajimas(pi_J_asc, J_asc[0], nJ))
del (J_asc[3])
res.extend(J_asc)
head = head + 'SegS_J_ASC\tSing_J_ASC\tDupl_J_ASC\tPi_J_ASC\tTajD_J_ASC\t'
M_asc = []
ss_M_asc = afs_stats_bitarray.base_S_ss(seqM_asc_bits, nM)
if (ss_M_asc[0] == 0):
for i in xrange(5):
M_asc.append(0)
pi_M_asc = 0
else:
M_asc.extend(afs_stats_bitarray.base_S_ss(seqM_asc_bits, nM))
pi_M_asc = afs_stats_bitarray.Pi2(M_asc[3], nM)
M_asc.append(pi_M_asc)
M_asc.append(afs_stats_bitarray.Tajimas(pi_M_asc, M_asc[0], nM))
del (M_asc[3])
res.extend(M_asc)
head = head + 'SegS_M_ASC\tSing_M_ASC\tDupl_M_ASC\tPi_M_ASC\tTajD_M_ASC\t'
EA_asc = []
ss_EA_asc = afs_stats_bitarray.base_S_ss(seqEA_asc_bits, nEA)
if (ss_EA_asc[0] == 0):
for i in xrange(5):
EA_asc.append(0)
pi_EA_asc = 0
else:
EA_asc.extend(afs_stats_bitarray.base_S_ss(seqEA_asc_bits, nEA))
pi_EA_asc = afs_stats_bitarray.Pi2(EA_asc[3], nEA)
EA_asc.append(pi_EA_asc)
EA_asc.append(afs_stats_bitarray.Tajimas(pi_EA_asc, EA_asc[0], nEA))
del (EA_asc[3])
res.extend(EA_asc)
head = head + 'SegS_EA_ASC\tSing_EA_ASC\tDupl_EA_ASC\tPi_EA_ASC\tTajD_EA_ASC\t'
WA_asc = []
ss_WA_asc = afs_stats_bitarray.base_S_ss(seqWA_asc_bits, nWA)
if (ss_WA_asc[0] == 0):
for i in xrange(5):
WA_asc.append(0)
pi_WA_asc = 0
else:
WA_asc.extend(afs_stats_bitarray.base_S_ss(seqWA_asc_bits, nWA))
pi_WA_asc = afs_stats_bitarray.Pi2(WA_asc[3], nWA)
WA_asc.append(pi_WA_asc)
WA_asc.append(afs_stats_bitarray.Tajimas(pi_WA_asc, WA_asc[0], nWA))
del (WA_asc[3])
res.extend(WA_asc)
head = head + 'SegS_WA_ASC\tSing_WA_ASC\tDupl_WA_ASC\tPi_WA_ASC\tTajD_WA_ASC\t'
res.append(afs_stats_bitarray.FST2(seqAf_asc_bits, pi_Af_asc, naf_CGI, seqEu_asc_bits, pi_Eu_asc, neu_CGI))
res.append(afs_stats_bitarray.FST2(seqAf_asc_bits, pi_Af_asc, naf_CGI, seqAs_asc_bits, pi_As_asc, nas_CGI))
res.append(afs_stats_bitarray.FST2(seqEu_asc_bits, pi_Eu_asc, neu_CGI, seqAs_asc_bits, pi_As_asc, nas_CGI))
head = head + 'FST_AfEu_ASC\tFST_AfAs_ASC_m\tFST_EuAs_ASC\t'
res.append(afs_stats_bitarray.FST2(seqEA_asc_bits, pi_EA_asc, nEA, seqWA_asc_bits, pi_WA_asc, nWA))
res.append(afs_stats_bitarray.FST2(seqEA_asc_bits, pi_EA_asc, nEA, seqEu_asc_bits, pi_Eu_asc, neu_CGI))
res.append(afs_stats_bitarray.FST2(seqEA_asc_bits, pi_EA_asc, nEA, seqJ_asc_bits, pi_J_asc, nJ))
res.append(afs_stats_bitarray.FST2(seqEA_asc_bits, pi_EA_asc, nEA, seqM_asc_bits, pi_M_asc, nM))
res.append(afs_stats_bitarray.FST2(seqM_asc_bits, pi_M_asc, nM, seqJ_asc_bits, pi_J_asc, nJ))
res.append(afs_stats_bitarray.FST2(seqWA_asc_bits, pi_WA_asc, nWA, seqEu_asc_bits, pi_Eu_asc, neu_CGI))
res.append(afs_stats_bitarray.FST2(seqWA_asc_bits, pi_WA_asc, nWA, seqJ_asc_bits, pi_J_asc, nJ))
res.append(afs_stats_bitarray.FST2(seqWA_asc_bits, pi_WA_asc, nWA, seqM_asc_bits, pi_M_asc, nM))
head = head + 'FST_eAwA_ASC\tFST_eAEu_ASC\tFST_eAJ_ASC\tFST_eAM_ASC\tFST_MJ_ASC\tFST_wAEu_ASC\tFST_wAJ_ASC\tFST_wAM_ASC\n'
filesummary='real_output_M23.summary'
filesumm=open(filesummary,'w')
filesumm.write(head)
out=''
for g in range(len(res)):
out=out+str(res[g])+'\t'
out=out[:-1]+'\n'
filesumm.write(out)
filesumm.close()
return res
if __name__ == '__main__':
main()