reorganise the main help with subcommands description

ppanggolin/main.py

@@ -60,32 +60,32 @@ def cmd_line() -> argparse.Namespace:
     desc += "  \n"
     desc += "  Expert:\n"
     desc += "    annotate      Annotate genomes\n"
-    desc += "    cluster       Cluster proteins in protein families\n"
+    desc += "    cluster       Cluster genes into gene families\n"
     desc += "    graph         Create the pangenome graph\n"
     desc += "    partition     Partition the pangenome graph\n"
     desc += "    rarefaction   Compute the rarefaction curve of the pangenome\n"
-    desc += "    msa           Compute Multiple Sequence Alignments for pangenome gene families\n"
-    desc += "    projection    Annotate an input genome with an existing pangenome\n"
-    desc += "    metadata      Add metadata to elements in pangenome\n"
+    desc += "    metadata      Add metadata to elements in yout pangenome\n"
     desc += "  \n"
     desc += "  Output:\n"
     desc += "    draw              Draw figures representing the pangenome through different aspects\n"
-    desc += "    write_pangenome:  Writes 'flat' files that represent the pangenome and its elements for use with other software.\n"
-    desc += "    write_genomes:    Writes 'flat' files that represent the genomes along with their associated pangenome elements.\n"
-    desc += "    fasta             Writes fasta files for different elements of the pangenome\n"
-    desc += "    info              Prints information about a given pangenome graph file\n"
-    desc += "    metrics           Compute several metrics on a given pangenome\n"
+    desc += "    write_pangenome   Writes 'flat' files that represent the pangenome and its elements for use with other software.\n"
+    desc += "    write_genomes     Writes 'flat' files that represent the genomes along with their associated pangenome elements.\n"
+    desc += "    fasta             Writes fasta files for different elements of the pangenome.\n"
+    desc += "    info              Prints information about a given pangenome graph file.\n"
+    desc += "    metrics           Compute several metrics on a given pangenome.\n"
     desc += "  \n"
-    desc += "  Regions of genomic Plasticity:\n"
-    desc += "    align        aligns a genome or a set of proteins to the pangenome gene families representatives and " \
-            "predict information from it\n"
-    desc += "    rgp          predicts Regions of Genomic Plasticity in the genomes of your pangenome\n"
-    desc += "    rgp_cluster  cluster RGPs based on their gene families.\n"
-    desc += "    spot         predicts spots in your pangenome\n"
-    desc += "    module       Predicts functional modules in your pangenome\n"
+    desc += "  Regions of Genomic Plasticity:\n"
+    desc += "    rgp           Predicts Regions of Genomic Plasticity in the genomes of your pangenome.\n"
+    desc += "    spot          Predicts spots in your pangenome.\n"
+    desc += "    module        Predicts functional modules in your pangenome.\n"
+    desc += "    rgp_cluster   Cluster RGPs based on their gene families.\n"
     desc += "  \n"
-    desc += "  Genomic context:\n"
-    desc += "    context      Local genomic context analysis\n"
+    desc += "  Analysis using reference pangenomes:\n"
+    desc += "    msa          Compute Multiple Sequence Alignments for pangenome gene families.\n"
+    desc += "    align        Aligns a genome or a set of proteins to the pangenome gene families and " \
+        "predicts information from it.\n"
+    desc += "    context      Local genomic context analysis.\n"
+    desc += "    projection   Annotates external genomes with an existing pangenome.\n"
     desc += "  \n"
     desc += "  Utility command:\n"
     desc += "    utils      Helper side commands.\n"