Require -o argument in design.py

README.md

@@ -98,15 +98,17 @@ To see details on all the arguments that the program accepts, run:
 design.py --help
 ```
 
-[`design.py`](./bin/design.py) requires one or more `dataset`s that specify input sequence data to target:
+[`design.py`](./bin/design.py) requires one or more `dataset`s that specify input sequence data to target, as well as a path to which the probe sequences are written:
 
 ```bash
-design.py [dataset] [dataset ...]
+design.py [dataset] [dataset ...] -o OUTPUT
 ```
 
 Each `dataset` can be a path to a FASTA file. If you [downloaded](#downloading-viral-sequence-data) viral sequence data, it can also simply be a label for one of [550+ viral datasets](./catch/datasets/README.md) (e.g., `human_immunodeficiency_virus_1` or `zika`) distributed as part of this package.
 Each of these datasets includes all available whole genomes (genome neighbors) in [NCBI's viral genome data](https://www.ncbi.nlm.nih.gov/genome/viruses/) for a species that has human as a host, as of Oct. 2018.
 
+The probe sequences are written to OUTPUT in FASTA format.
+
 Below is a summary of some useful arguments to `design.py`:
 
 * `-pl PROBE_LENGTH`/`-ps PROBE_STRIDE`: Design probes to be PROBE_LENGTH nt long, and generate candidate probes using a stride of PROBE_STRIDE nt.
@@ -136,7 +138,6 @@ If not set, CATCH uses its default model of hybridization based on `-m/--mismatc
 * `--filter-with-lsh-hamming FILTER_WITH_LSH_HAMMING`/`--filter-with-lsh-minhash FILTER_WITH_LSH_MINHASH`: Use locality-sensitive hashing to reduce the space of candidate probes.
 This can significantly improve runtime and memory requirements when the input is especially large and diverse.
 See `design.py --help` for details on using these options and downsides.
-* `-o OUTPUT`: Write probe sequences in FASTA format to OUTPUT.
 
 ### Pooling across many runs ([`pool.py`](./bin/pool.py))
 

bin/design.py

@@ -275,9 +275,8 @@ def main(args):
                                       allow_small_seqs=args.small_seq_min)
     pb.design()
 
-    if args.output_probes:
-        # Write the final probes to the file args.output_probes
-        seq_io.write_probe_fasta(pb.final_probes, args.output_probes)
+    # Write the final probes to the file args.output_probes
+    seq_io.write_probe_fasta(pb.final_probes, args.output_probes)
 
     if (args.print_analysis or args.write_analysis_to_tsv or
             args.write_sliding_window_coverage):
@@ -320,6 +319,12 @@ def main(args):
               "'collection:' (e.g., 'collection:viruses_with_human_host'), "
               "then this reads from an available collection of datasets."))
 
+    # Outputting probes
+    parser.add_argument('-o', '--output-probes',
+        required=True,
+        help=("The file to which all final probes should be "
+              "written; they are written in FASTA format"))
+
     # Parameters on probe length and stride
     parser.add_argument('-pl', '--probe-length',
         type=int,
@@ -473,11 +478,7 @@ def check_coverage(val):
               "are blacklisted. See --custom-hybridization-fn for details "
               "of how this function should be implemented and provided."))
 
-    # Outputting probe sequences and coverage analyses
-    parser.add_argument('-o', '--output-probes',
-        help=("(Optional) The file to which all final probes should be "
-              "written; if not specified, the final probes are not "
-              "written to a file"))
+    # Outputting coverage analyses
     parser.add_argument('--print-analysis',
         dest="print_analysis",
         action="store_true",