arg_parser.add_argument("--distance_cutoff", help="r2, or kb distance") args = arg_parser.parse_args() # # Create directories and logging dirs: # #ShellUtils.mkdirs(args.output_dir_path) if args.distance_type == "ld": output_dir_path = args.output_dir_path+"/ld"+str(args.distance_cutoff) ld_cutoff = args.distance_cutoff if args.distance_type == "kb": output_dir_path = args.output_dir_path+"/kb"+str(args.distance_cutoff) kb_cutoff = args.distance_cutoff ShellUtils.mkdirs(output_dir_path + "/snplists/") ShellUtils.mkdirs(output_dir_path + "/ldlists/") log_dir_path = output_dir_path + "/log" # Pascal - FIXED ERROR. : before it was /log/ ShellUtils.mkdirs(log_dir_path) print("Running with %s option, using cutoff %s"%(args.distance_type,args.distance_cutoff)) # #prepare queue parameters and commands # ##TODO@@ Adjust queue parameters?? queue_name = "cbs" #walltime="604800" # 60*60*24*7=7 days #walltime="86400" # 60*60*24=1 day mem_per_job="10gb" #=>> PBS: job killed: mem job total 4323312 kb exceeded limit 3145728 kb flags = "sharedmem"
print "The genotype_prefix is set to: %s" % genotype_prefix print "You will overwrite files in /snplists and /ldlists if the parameters in step1/ and step2/ do not match" print "Plese confirm that this is the correct paths to use by typing 'yes'" while ans != 'yes': ans = raw_input("Confirm: ") print "Ok let's start..." ######### Non-finished statement for checking if /snplists path. ####### # if True: # snp_list_dir = os.path.join(output_dir_path, "snplists") # if os.listdir(snp_list_dir): # directory is NOT empty # print "It apears that the /snplists path is non-empty" ######################################################################### ShellUtils.mkdirs(output_dir_path + "/snplists/") #TODO: remove trailing slash and see if it still works ShellUtils.mkdirs(output_dir_path + "/ldlists/") #TODO: remove trailing slash and see if it still works log_dir_path = output_dir_path + "/log" # Pascal - FIXED ERROR. : before it was /log/ ShellUtils.mkdirs(log_dir_path) print("Running with %s option, using cutoff %s"%(args.distance_type,args.distance_cutoff)) # #prepare queue parameters and commands # ##TODO@@ Adjust queue parameters?? queue_name = "idle" # default - 06/15/2014 #queue_name = "idle" walltime="604800" # 60*60*24*7=7 days #walltime="86400" # 60*60*24=24 hours - 06/15/2014 #mem_per_job="15gb" #=>> PBS: job killed: mem job total 4323312 kb exceeded limit 3145728 kb
# Parse arguments arg_parser = argparse.ArgumentParser(description="Run parse_matched_SNPs.py") arg_parser.add_argument("--plink_matched_snps_path", \ help="""Path for plink_matched_snps.py results which contain 3 directories [ldlists, log, snplists], e.g. /home/projects/tp/childrens/snpsnap/data/step2/1KG_full_queue/ld0.5/ NB. please use symlinks in the path, i.e. do not use /net/home...""", required=True) #NB. Also check that the path has a trailing slash (/) args = arg_parser.parse_args() path = os.path.abspath(args.plink_matched_snps_path) # Trailing slash are removed/corrected - NICE! #^^^ E.g. "/home/projects/tp/tools/matched_snps/src/hapmap/ld0.5/" #^^^ E.g. "/home/projects/tp/childrens/snpsnap/data/step2/1KG_test_thin0.1/ld0.5/" log_dir_path = path + "/log" #PASCAL: PROBLEM fixed with extra slash stat_gene_density_path = path + "/stat_gene_density" ShellUtils.mkdirs(stat_gene_density_path) ### Make sure that the genotype prefix is correct ### if False: ans = "" print "*** SAFETY CHECK! ***" print "You specifed --plink_matched_snps_path to be: %s" % args.plink_matched_snps_path #print "NB Please check that the path has a trailing slash (/) - It may not work without - FIX THIS!" print "Plese confirm that this is the correct path to use by typing 'yes'" while ans != 'yes': ans = raw_input("Confirm: ") print "Ok let's start..." submit(path, stat_gene_density_path)