def tier(args, annotation_joined_outfile, yaml_cmds, output_dir=None, tier_name='Global'): ## MAIN CODE print 'Performing variant prioritization' if(output_dir == None): output_dir = os.path.join(args.output_dir, 'tiering_allvars') else: output_dir = os.path.join(output_dir, 'tiering_allvars') # targeted tiering only if BAM file provided? (TODO) # stmp_tiering_util.tiers_target(os.path.join(args.output_dir, 'tiers_target.tsv'), os.path.join(args.output_dir, 'tiers_target'), args.target_genes, pop=args.ethnicity) # standard VCF prioritization (tiering) stmp_tiering_util.tiers_allvars(annotation_joined_outfile, output_dir, args.target_genes, pop=args.ethnicity, yaml_cmds=yaml_cmds)
def tier(args, annotation_joined_outfile, yaml_cmds):
## MAIN CODE
print 'Performing variant prioritization'
# targeted tiering only if BAM file provided?
# stmp_tiering_util.tiers_target(os.path.join(args.output_dir, 'tiers_target.tsv'), os.path.join(args.output_dir, 'tiers_target'), args.target_genes, pop=args.ethnicity)
# standard VCF prioritization (tiering)
stmp_tiering_util.tiers_allvars(joined_outfile, os.path.join(args.output_dir, 'tiering_allvars'), args.target_genes, pop=args.ethnicity, yaml_cmds=yaml_cmds)
if args.sfs_file != "None":
for i in range(1,5):
stmp_tiering_util.filter_sfs(os.path.join(args.output_dir, "allvars.tier"+str(i)+".txt"), args.sfs_file, os.path.join(args.output_dir, "allvars.tier"+str(i)+"-sfs_filtered.txt"), 2)
print("Done with variant prioritization. Check output files in " + args.output_dir)
def tier(args, annotation_joined_outfile, yaml_cmds, output_dir=None, tier_name='Global'): ## MAIN CODE print 'Performing variant prioritization' if(output_dir == None): output_dir = os.path.join(args.output_dir, 'tiering_allvars') else: output_dir = os.path.join(output_dir, 'tiering_allvars') # targeted tiering only if BAM file provided? (TODO) # stmp_tiering_util.tiers_target(os.path.join(args.output_dir, 'tiers_target.tsv'), os.path.join(args.output_dir, 'tiers_target'), args.target_genes, pop=args.ethnicity) # standard VCF prioritization (tiering) stmp_tiering_util.tiers_allvars(annotation_joined_outfile, output_dir, args.target_genes, pop=args.ethnicity, yaml_cmds=yaml_cmds) # SFS filtering (TODO) if args.sfs_file != "None": print 'Performing SFS filtering (check output at ' + str(output_dir) + ')' for i in range(1,5): stmp_tiering_util.filter_sfs(output_dir+'.tier'+str(i)+'.txt', args.sfs_file, output_dir+'.tier'+str(i)+"-sfs_filtered.txt", 2)