#!/usr/bin/env python

from annopred import pred_main, LD_PyWrapper, prior_generating, coord_trimmed

if __name__ == '__main__':
  print(pred_main.main)
  print(LD_PyWrapper.callLDSC)
  print(prior_generating.generate_h2_pT)
  print(prior_generating.generate_h2_from_user)
  print(coord_trimmed.main)

@@ -16,16 +16,52 @@
 python%0A%0A
+from argparse import ArgumentParser%0A
 from ann
@@ -135,34 +135,2173 @@
 ed%0A%0A
-if __name__ == '__main__':
+# Create the master argparser and returns the argparser object%0Adef get_argparser():%0A  parser = ArgumentParser(prog=%22AnnoPred%22, %0A                          description=%22Genetic Risk Prediction Software%22)%0A  ## Input Files%0A  #################### %0A  # GWAS sumstats%0A  parser.add_argument('--sumstats', required=True, help=%22GWAS summary stats%22)%0A  # Reference Genotype%0A  parser.add_argument('--ref_gt', required=True, %0A                      help=%22Reference genotype, plink bed format%22)%0A  # Validation Genotype%0A  parser.add_argument('--val_gt', required=True, %0A                      help=%22Validation genotype, plink bed format%22)%0A%0A  # For LDSC%0A  parser.add_argument('--N_case', required=True, type=int,%0A                      help=%22Number of cases in GWAS training, for LDSC%22)%0A  parser.add_argument('--N_ctrl', required=True, type=int,%0A                      help=%22Number of ctrls in GWAS training, for LDSC%22)%0A%0A  # For Pred%0A  parser.add_argument('--P', required=True, type=float,%0A                      help=%22Tuning parameter in (0,1)%22%0A                           %22, the proportion of causal snps%22)%0A  # Local LD file%0A  parser.add_argument('--local_ld_prefix', default=%22test_local_ld%22,%0A                      help=%22A local LD file name prefix%22%0A                           %22, will be created if not present%22)%0A  # Optional%0A  parser.add_argument('--ld_radius', type=int,%0A                      help=%22If not provided, will use the number of SNPs in%22 %0A                           %22 common divided by 3000%22)%0A  parser.add_argument('--per_SNP_h2', %0A                      help=%22Path to per-SNP heritability.%22%0A                           %22 If not provided, will use LDSC with 53 baseline%22%0A                           %22 annotations, GenoCanyon and GenoSkyline.%22)%0A%0A  ## Output Files%0A  #####################%0A  # Coord output H5 file %0A  parser.add_argument('--coord_out', default=%22coord_out.h5%22, %0A                      help=%22Output H5 File for coord_genotypes%22)%0A  # Output results%0A  parser.add_argument('--out', default=%22AnnoPred_out%22,%0A                      help=%22Output filename prefix for AnnoPred%22)%0A%0A  return parser%0A%0A%0Aif __name__ == '__main__':%0A  args = get_argparser().parse_args()%0A  print(args)
 %0A  p

define argparser