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(argv): global out_base, freq_loc, meta_loc, bfile, table_type global covar_loc, annot, weight_min, build, fix_args global family cl_arguments(argv) #fix_it.main(fix_args) gene_region_list = pc_toolbox.create_region_list(region_loc) annot_dict_loc = fix_it.locate_annot_dict(build) ## print annot_dict_loc annot_dict = fix_it.build_annot_dict('LOG',annot_dict_loc) ## print("Annotation Dictionary as Follows:") ## print annot_dict ## gene_list = sorted(key_list,key=lambda gene:gene_region_dict[gene][0]) #head, tail = os.path.split(out_file) #keep_loc = os.path.join(out_file,'_plink_keep.txt') keep_loc = out_base+'_plink_keep.txt' plink_out = out_base+'_sigs_inCC' #fixed_meta_loc = fix_it.locate_fixed_meta(meta_loc, build) ## print fixed_meta_loc fixed_meta_loc = meta_loc index_dict = create_index_dict(fixed_meta_loc,table_type) z_list, lw_list = find_leastP_SNPs(gene_region_list, fixed_meta_loc, index_dict, out_base, freq_loc, keep_loc, weight_min, table_type, annot_dict) if bfile is not None and covar_loc is not None: plink_it(keep_loc, bfile, covar_loc, plink_out) repair_for_zs(z_list, lw_list, fixed_meta_loc, index_dict, build)
def which_one(region_loc, table_loc,chromosome, index_dict, zero_list): if region_loc is not None: ## determine_table_titles(table_loc) ## region_list = create_region_list(region_loc, region_col_dict) mb_region_list = pc_toolbox.create_region_list(region_loc) region_list = list() for mb_region in mb_region_list: region = RegInfo(chro = mb_region.chro, start = int(float(mb_region.start) * 1e6), end = int(float(mb_region.end) *1e6), band=mb_region.band, sym=mb_region.sym, ID=mb_region.ID,title=mb_region.title) region_list.append(region) print region_list else: range_list = macro_ranges(table_loc, chromosome, index_dict) ## print(range_list) region_list = macro_regions(chromosome, range_list) ## base, ext = os.path.splitext(table_loc) ## noZ_loc = base + '_noZs'+ext fix_list, zr_list = identify_zerops(region_list, zero_list) print(''' ************************************************************************************ Here are the regions which will be drawn: ''') for fix in fix_list: print fix print(''' The following regions contain zero p-values, and will be adapted:''') for z in zr_list: print z print(''' ************************************************************************************''') sys.stdout.flush() return fix_list, zr_list
def main(): global out_file, region_loc,assoc_loc, freq_loc cl_arguments(sys.argv[1:]) gene_region_list = pc_toolbox.create_region_list(region_loc) #gene_region_dict = create_region_dict(region_loc,position_form) #key_list = gene_region_dict.keys() #gene_list = sorted(key_list,key=lambda gene:gene_region_dict[gene][0]) #find_leastP_SNPs(gene_list, gene_region_dict, assoc_loc) find_leastP_SNPs(gene_region_list, assoc_loc, out_file, freq_loc)
def main(argv): region_loc = REGION_LOC build = BUILD meta_loc = META_LOC outfolder = OUTFOLDER region_list = pc_toolbox.create_region_list(region_loc) annot_dict_loc = fix_it.locate_annot_dict(build) annot_dict = fix_it.build_annot_dict('LOG',annot_dict_loc) fixed_meta_loc = fix_it.locate_fixed_meta(meta_loc, build) for region in region_list: read_meta(fixed_meta_loc, region, outfolder, build, annot_dict)
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 main(argv): global region_loc, pc_cmdlist print sys.argv cl_arguments(argv) print(pc_cmdlist) ## gene_region_dict = pc_toolbox.create_region_dict(region_loc, POSITION_FORM) ## key_list = gene_region_dict.keys() ## print gene_region_dict ## index_tup = (chrcol,startcol,endcol,genecol) ## region_list = create_region_list(region_loc, index_tup) region_list = pc_toolbox.create_region_list(region_loc) for region in region_list: cmd = write_command(region, pc_cmdlist) os.system(cmd)
def main(): global out_file, table_loc, assoc, region_loc, build cl_arguments(sys.argv[1:]) region_list = pc_toolbox.create_region_list(region_loc) annot_dict_loc = fix_it.locate_annot_dict(build) purpose = 'LOG' annot_dict = fix_it.build_annot_dict(purpose,annot_dict_loc) ## annot_dict = None ## print("Annotation Dictionary as Follows:") ## print annot_dict ## if annot is not None: ## annot_dict = meta_toolbox.read_annot(annot) ## elif fix: ## annot_dict = meta_toolbox.read_annot_dict() snp_list = read_table(table_loc, region_list, assoc, annot_dict) print("inter_region_yank finds {0} SNPs of significance!".format(len(snp_list))) write_results(snp_list, out_file, assoc, annot_dict)
def which_one(region_loc, table_loc,chromosome, index_dict, zero_list): if region_loc is not None: ## determine_table_titles(table_loc) ## region_list = create_region_list(region_loc, region_col_dict) mb_region_list = pc_toolbox.create_region_list(region_loc) region_list = [] for mb_region in mb_region_list: region = RegInfo(chro = mb_region.chro, start = int(float(mb_region.start) * 1e6), end = int(float(mb_region.end) *1e6), band=mb_region.band, sym=mb_region.sym) region_list.append(region) print region_list else: range_list = macro_ranges(table_loc, chromosome, index_dict) ## print(range_list) region_list = macro_regions(chromosome, range_list) fix_list = remove_zerops(region_list, zero_list) print('Here are the regions which will be drawn:') print fix_list return fix_list
def main(argv): global region_loc, pc_cmdlist, cluster, cflag print sys.argv cl_arguments(argv) print(pc_cmdlist) ## gene_region_dict = pc_toolbox.create_region_dict(region_loc, POSITION_FORM) ## key_list = gene_region_dict.keys() ## print gene_region_dict ## index_tup = (chrcol,startcol,endcol,genecol) ## region_list = create_region_list(region_loc, index_tup) region_list = pc_toolbox.create_region_list(region_loc) for region in region_list: cmd = write_command(region, pc_cmdlist) if cluster: bash_loc = './PBS_scripts/'+region+'_'+cflag+'.sh' print bash_loc #write_bash(bash_loc, cmd) #os.system('qsub {0}.'.format(bash_loc)) else: os.system(cmd)
def main(argv): global out_base, freq_loc, table_loc, bfile, table_type global covar_loc, annot, weight_min, build, region_loc, pop, aa_freq_loc cl_arguments(argv) zlist = list() index_dict, input_title_line = pc_toolbox.create_index_dict(table_loc, table_type) region_list = pc_toolbox.create_region_list(region_loc) annot_dict = create_annot_dict(build, 'LOG') out_file = out_base + '_yank.tbl' output_title_line = create_output_title_line(table_type, input_title_line) with open(out_file, mode="w") as out_text: ## title_line = '\t'.join(META_TITLE_LIST) out_text.write(output_title_line +'\n') for region in region_list: print zlist sig_line, zlist, multicounter = read_table(table_loc, index_dict, region, weight_min, table_type, annot_dict, zlist) info = document_result(sig_line, region, index_dict, table_type,annot_dict, multicounter) if table_type == 'assoc': if pop == 'AA': for item in AA_ASSOC_ORDER_LIST: out_text.write(str(info[item]) + '\t') if pop == 'UK': for item in ASSOC_ORDER_LIST: out_text.write(str(info[item]) + '\t') ## if table_type in ['perm']: ## out_list = sig_line.strip().split() ## out_list.append(info['note']) ## out_list.append(info['band']) ## out_list.append(info['ID']) ## out_text.write('\t'.join(out_list)) if table_type in ['meta','family']: for item in META_ORDER_LIST: out_text.write(str(info[item]) + '\t') if table_type =='perm': for item in PERM_ORDER_LIST: out_text.write(str(info[item]) + '\t') out_text.write('\n') if table_type in ['meta','family']: repair_meta_for_lz(zlist, table_loc, index_dict, weight_min)