def create_command(lz_cmdlist, outfolder, logname, chromosome=None): cmd_list = ["python lz_meta.py"] cmd_list.extend(lz_cmdlist) if chromosome is not None: c_cmd = ["--chromosome",str(chromosome)] cmd_list.extend(c_cmd) #locate log folder lf = pc_toolbox.log_folder(outfolder) log_file = os.path.join(lf,logname) #add log command t_cmd = ["2>&1|tee",log_file] cmd_list.extend(t_cmd) cmd = ' '.join(cmd_list) print ('My log file is {0} and my command is {1}'.format(log_file,cmd)) return cmd
def create_command(script_loc , pheno_tag=None): global chromosome,range_start_bp,range_end_bp,plink_test global p_bound, pheno_loc, c_interval, chrband, build global output_folder, maxloops, out_flag, condition_list, interrupt cmd_list = ["python pc_workhorse.py","--chromosome",chromosome, "--from-bp", str(range_start_bp),"--to-bp", str(range_end_bp), "--pbound",str(p_bound), "--test", plink_test, "--script", script_loc, "--outfolder",output_folder, "--loop",str(maxloops), "--build",build] ## if interrupt: ## cmd_list.extend(['--interrupt']) of = "" if out_flag is not None: of = '_'+out_flag f_cmd = ["--flag",out_flag] cmd_list.extend(f_cmd) logname = "" log_start = 'Chr'+chromosome+'_' ## if refgene is not None: ## r_cmd = ["--refgene",refgene] ## cmd_list.extend(r_cmd) if chrband is None: log_start = 'Chr'+chromosome+'_' if refgene is None: r_start = convert_bp_to_mb(range_start_bp) r_end = convert_bp_to_mb(range_end_bp) logname =log_start + r_start + '-'+r_end+of else: logname = log_start + refgene+of else: logname = chrband + of b_cmd = ["--chrband",chrband] cmd_list.extend(b_cmd) lf = pc_toolbox.log_folder(output_folder) #log_file = os.path.join(lf,log) if pheno_tag is not None: logname = logname + '_'+pheno_tag p_cmd = ["--pheno-tag",pheno_tag] cmd_list.extend(p_cmd) ci_cmd = [] if c_interval is None and plink_test in ('logistic', 'linear','assoc', 'fisher'): c_interval = C_INTERVAL if c_interval is not None: ci_cmd = ["--ci",str(c_interval)] cmd_list.extend(ci_cmd) t_cmd = [] if condition_list is None: log = logname + '.log' log_file = os.path.join(lf,log) t_cmd = ["2>&1|tee",log_file] elif interrupt: cmd_list.extend(['--interrupt']) c_cmd = ["--condition-list",condition_list] cmd_list.extend(c_cmd) if '~' in condition_list: log = logname + '~.log' else: log = logname + '.log' log_file = os.path.join(lf,log) t_cmd = ["2>&1|tee -a",log_file] else: c_cmd = ["--condition-list",condition_list] cmd_list.extend(c_cmd) log = logname + '~.log' log_file = os.path.join(lf,log) t_cmd = ["2>&1|tee",log_file] #t_cmd = ["2>&1|tee",log_file] cmd_list.extend(t_cmd) cmd = ' '.join(cmd_list) print ('My log file is {0} and my command is {1}'.format(log_file,cmd)) return cmd