Improvements to sourmash argparse output for compute. (#931)

* an initial usage description for sourmash compute

* fix so that sourmash, and sourmash compute, display the right thing

* shorten sourmash default output

* revise language a bit

Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>

sourmash/cli/compare.py

@@ -1,4 +1,4 @@
-"""compare genomes"""
+"""compare sequence signatures made by compute"""
 
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 

sourmash/cli/compute.py

@@ -1,4 +1,30 @@
-"""compute genome signatures"""
+"""compute sequence signatures for inputs"""
+
+usage="""
+
+   sourmash compute -k 21,31,51 *.fa *.fq
+
+Create MinHash sketches at k-mer sizes of 21, 31 and 51, for
+all FASTA and FASTQ files in the current directory, and save them in
+signature files ending in '.sig'. You can rapidly compare these files
+with `compare` and query them with `search`, among other operations;
+see the full documentation at http://sourmash.rtfd.io/.
+
+The key options for compute are:
+
+ * `-k/--ksize <int>[, <int>]: k-mer size(s) to use, e.g. -k 21,31,51
+ * `-n/--num <int>` or `--scaled <int>`: set size or resolution of sketches
+ * `--track-abundance`: track abundances of hashes (default False)
+ * `--dna or --protein`: nucleotide and/or protein signatures (default `--dna`)
+ * `--merge <name>`: compute a merged signature across all inputs.
+ * `--singleton`: compute individual signatures for each sequence.
+ * `--name-from-first`: set name of signature from first sequence in file.
+ * `-o/--output`: save all computed signatures to this file.
+
+Please see -h for all of the options as well as more detailed help.
+
+---
+"""
 
 from argparse import FileType
 
@@ -18,7 +44,7 @@ def ksize_parser(ksizes):
 
 
 def subparser(subparsers):
-    subparser = subparsers.add_parser('compute')
+    subparser = subparsers.add_parser('compute', description=__doc__, usage=usage)
 
     sketch_args = subparser.add_argument_group('Sketching options')
     sketch_args.add_argument(

sourmash/cli/gather.py

@@ -1,5 +1,4 @@
-"""search a metagenome signature for multiple non-
-                                  overlapping matches"""
+"""search a metagenome signature against dbs"""
 
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 

sourmash/cli/search.py

@@ -1,4 +1,4 @@
-"""search a signature against a list of signatures"""
+"""search a signature against other signatures"""
 
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args