Merged Tanya's files + final lint check

term_frag_sel/cli.py

@@ -35,8 +35,8 @@ def main(args: argparse.Namespace):
         fasta_dict = fasta_parse[split:splits[i+1]]
         term_frags = fragmentation(fasta_dict, seq_counts,
                                    args.mean, args.std,
-                                   args.A_prob, args.T_prob,
-                                   args.G_prob, args.C_prob)
+                                   args.a_prob, args.t_prob,
+                                   args.g_prob, args.c_prob)
 
         logger.info("Writing batch %s sequences to %s...", i, args.output)
         with open(args.output, 'a', encoding="utf-8") as out_file:
@@ -97,21 +97,21 @@ def parse_arguments() -> argparse.Namespace:
                         help="output file path")
     parser.add_argument('--mean', required=False, default=300,
                         type=check_positive,
-                        help="Mean fragment length (default: 10)")
+                        help="Mean fragment length (default: 300)")
     parser.add_argument('--std', required=False, default=60,
                         type=check_positive,
                         help="Standard deviation fragment length \
-                            (defafult: 1)")
-    parser.add_argument('-a', '--A_prob', required=False, default=0.22,
+                            (defafult: 60)")
+    parser.add_argument('-a', '--a_prob', required=False, default=0.22,
                         type=check_prob,
                         help="Probability cut happens after nucleotide A")
-    parser.add_argument('-t', '--T_prob', required=False, default=0.25,
+    parser.add_argument('-t', '--t_prob', required=False, default=0.25,
                         type=check_prob,
                         help="Probability cut happens after nucleotide T")
-    parser.add_argument('-g', '--G_prob', required=False, default=0.25,
+    parser.add_argument('-g', '--g_prob', required=False, default=0.25,
                         type=check_prob,
                         help="Probability cut happens after nucleotide G")
-    parser.add_argument('-c', '--C_prob', required=False, default=0.28,
+    parser.add_argument('-c', '--c_prob', required=False, default=0.28,
                         type=check_prob,
                         help="Probability cut happens after nucleotide C")
     parser.add_argument('-s', '--size', required=False, default=10000,