def tier_real(args, joined_outfile, yaml_commands): #tiering is separate tiering_output_dirs = [] # 1. candidate genes (user-specified target gene list) if(args.target_genes != None): args.target_genes = general_utils.root_or_cwd(args.target_genes) candidate_out_dir = os.path.join(args.output_dir, 'Candidate') if(not os.path.isdir(candidate_out_dir)): os.makedirs(candidate_out_dir) print 'Tiering candidate genes (user-specified)' tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=candidate_out_dir) tiering_output_dirs.append(candidate_out_dir) # 2. global global_tiering_out_dir = os.path.join(args.output_dir, 'Global') if(not os.path.isdir(global_tiering_out_dir)): os.makedirs(global_tiering_out_dir) args.target_genes = None # forces global tiering (no filtering based on a certain gene list) print 'Tiering all genes (Global)' tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=global_tiering_out_dir) tiering_output_dirs.append(global_tiering_out_dir) #3. other gene lists (specified in YAML) tiering_gene_lists = yaml_commands[yaml_keys.kModules][yaml_keys.kTiering][yaml_keys.kTTargetGeneLists] for tiering_gene_list in tiering_gene_lists: # ignore all "clinical" gene lists if we are suppressing incidental findings (e.g. for family members) if(args.suppress_incidentals and 'clinical' in tiering_gene_list.lower()): print 'Note: Skipping tiering for ' + str(tiering_gene_list) + ' to avoid incidental findings.' continue #else out_dir = os.path.join(args.output_dir, tiering_gene_list) if(not os.path.isdir(out_dir)): os.makedirs(out_dir) args.target_genes = yaml_utils.get_abs_path(tiering_gene_lists[tiering_gene_list]) print 'Tiering ' + str(tiering_gene_list) + ' genes' tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=out_dir) tiering_output_dirs.append(out_dir) # Generate final output as excel workbook final_tiering_out_file_path = stmp_tiering_util.tiers2xls(tiering_output_dirs, args.output_dir, yaml_commands) print '**** Tiering output written to ' + str(final_tiering_out_file_path) + ' *****' return final_tiering_out_file_path
def tier_real(args, joined_outfile, yaml_commands): #tiering is separate tiering_output_dirs = [] # 1. candidate genes (user-specified target gene list) if(args.target_genes != None): args.target_genes = general_utils.root_or_cwd(args.target_genes) candidate_out_dir = os.path.join(args.output_dir, 'Candidate') if(not os.path.isdir(candidate_out_dir)): os.makedirs(candidate_out_dir) tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=candidate_out_dir) tiering_output_dirs.append(candidate_out_dir) # 2. global global_tiering_out_dir = os.path.join(args.output_dir, 'Global') if(not os.path.isdir(global_tiering_out_dir)): os.makedirs(global_tiering_out_dir) args.target_genes = None # forces global tiering (no filtering based on a certain gene list) tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=global_tiering_out_dir) tiering_output_dirs.append(global_tiering_out_dir) #3. other gene lists (specified in YAML) tiering_gene_lists = yaml_commands[yaml_keys.kModules][yaml_keys.kTiering][yaml_keys.kTTargetGeneLists] for tiering_gene_list in tiering_gene_lists: out_dir = os.path.join(args.output_dir, tiering_gene_list) if(not os.path.isdir(out_dir)): os.makedirs(out_dir) args.target_genes = yaml_utils.get_abs_path(tiering_gene_lists[tiering_gene_list]) tier(args, joined_outfile, yaml_cmds=yaml_commands, output_dir=out_dir) tiering_output_dirs.append(out_dir) # Generate final output as excel workbook final_tiering_out_file_path = stmp_tiering_util.tiers2xls(tiering_output_dirs, args.output_dir) print '**** Tiering output written to ' + str(final_tiering_out_file_path) + ' *****' return final_tiering_out_file_path
