def main(argv): out_folder = '/home/jkb4y/cphgdesk_share/Yan/UBASH3A' eurmeta_out = os.path.join(out_folder, 'eurmeta_UBASH3A_122112.txt') eurmeta_in = '/home/jkb4y/work/data/2012Feb1/eurmeta_Oct2012/eurmeta_lz_hg19_intersect.tbl' eurmeta_dict, thing = pc_toolbox.create_index_dict(eurmeta_in, 'meta') family_out = os.path.join(out_folder, 'eurgdtscan_UBASH3A_122112.txt') family_in = '/home/jkb4y/work/data/2012Feb1/Family_Nov2012/eurgdtscan_lz_hg19_intersect.txt' family_dict, thing = pc_toolbox.create_index_dict(family_in, 'family') region_loc ='/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012.txt' region_list = pc_toolbox.create_bp_region_list(region_loc) for region in region_list: if region.ID == '21q22.3_a': print region filter_by_region(region, eurmeta_in,eurmeta_out, eurmeta_dict) filter_by_region(region, family_in, family_out, family_dict)
def main(): build = 'hg19' table_loc = '/home/jkb4y/ubs/work/results/July2012/Logistic_pc8/AA_8.assoc.logistic' annot_dict = pc_toolbox.create_annot_dict(build,'LOG') base, ext = os.path.splitext(table_loc) base2, ext2 = os.path.splitext(base) new_loc = base2 + '_lz'+ext2+ext index_dict, line = pc_toolbox.create_index_dict(table_loc,'assoc') pc_toolbox.give_table_annotation(table_loc,new_loc,index_dict,annot_dict)
def main(argv): global table_type, region_loc, cell_type, table_loc, perm, build, population build = 'hg19' cis = True population = 'EUR' region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_05242012_extra.5MB.txt' prelude_base = '/home/jkb4y/h4t1/programs/achilleas_plots/gene_prelude.R' cell_type = "CD8" postlude_folder= '/home/jkb4y/h4t1/programs/achilleas_plots/postludes' tablefold = '/home/jkb4y/ubs/work/data/Achilleas/cis-eQTL/' table_loc = os.path.join(tablefold,'{0}_cis_eqtls_permwBP_JB_LZ.txt'.format(cell_type)) table_type = 'perm' index_dict, thing = pc_toolbox.create_index_dict(table_loc, table_type) perm = True achilleas_cell_results = "/home/jkb4y/ubs/work/results/Achilleas/hg19/{0}".format(cell_type) genefolder = os.path.join(achilleas_cell_results,'GeneLists') base_outfolder = os.path.join(achilleas_cell_results, 'PerGene') if not os.path.exists(base_outfolder): os.makedirs(base_outfolder) regions = pc_toolbox.create_bp_region_list(region_loc) for region in regions: ID = region.ID band = region.band outfolder = os.path.join(base_outfolder, ID) if not os.path.exists(outfolder): os.makedirs(outfolder) os.chdir(outfolder) region_genefolder = os.path.join(genefolder, ID) genelist = os.path.join(region_genefolder, ID+'_genes.list') genes = read_list(genelist) for gene in genes: ## outfolder = os.path.join(base_outfolder, region.ID) ## if not os.path.exists(outfolder): ## os.makedirs(outfolder) refsnp_loc = os.path.join(region_genefolder, gene + '_ref.txt') refsnp = read_single(refsnp_loc) gene_prelude = locate_prelude(outfolder, gene, cell_type, ID) cell_postlude = None#locate_postlude(cell_type, postlude_folder) write_prelude(prelude_base, gene, gene_prelude) graph_title = create_title(cell_type, ID, gene) prefix = create_prefix(cell_type, band, gene, perm, cis) ## os.chdir(outfolder) locuszoom(table_loc, region,graph_title, index_dict, outfolder, refsnp, prefix, gene_prelude, cell_postlude) os.chdir(base_outfolder) try: os.rmdir(outfolder) except OSError: pass
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)