small fixes

SConstruct

@@ -760,6 +760,7 @@ def add_cluster_analysis(w):
 
         @w.add_target()
         def indel_fasttree_svg(outdir, c):
+            """create graphic showing indel-matching (matching uid passed in --show-indel-in-trees) in the fasttree as red"""
             indel_svg = env.Command(
                 path.join(
                     outdir,
@@ -836,6 +837,7 @@ def add_cluster_analysis(w):
 
         @w.add_target()
         def pruned_fasttree_png(outdir, c):
+            """create png showing included seqs (kept in pruning) as red"""
             if c["cluster"].get("size") < 4500:
                 pruned_cluster_fasttree_png = env.Command(
                     path.join(outdir, "pruned_cluster_fasttree.png"),
@@ -1062,6 +1064,7 @@ def add_cluster_analysis(w):
 
         @w.add_target()
         def indel_mltree_svg(outdir, c):
+            """create graphic showing indel-matching (matching uid passed in --show-indel-in-trees) in the max-likelihood tree as red"""
             indel_svg = env.Command(
                 path.join(
                     outdir, "{}_indel_mltree.svg".format(options["show_indel_in_trees"])

bin/annotate_tree.py

@@ -8,7 +8,7 @@
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Annotate tree with ids.")
     parser.add_argument("tree_path", type=str, help="Path to tree file.")
-    parser.add_argument("ids_path", type=str, help="Path to prune id file.")
+    parser.add_argument("ids_path", type=str, help="Path to file containing ids to annotate.")
     parser.add_argument(
         "--set-root",
         action="store_true",

bin/process_partis.py

@@ -666,7 +666,7 @@ def existing_file(fname):
     )
     seqs_args.add_argument(
         "--show-indel-in-trees",
-        help="create tree graphics highlighting in red any sequences on the tree with indels matching the indel in the sequence corresponding to the uid passed here in the annotation chosen in choose_cluster()",
+        help="add a column to --seqmeta-out to record which sequences have indels matching the indel in the sequence corresponding to the uid passed here in the annotation chosen in choose_cluster(). This info can be used to, for example, annotate tree graphics with indel information (as in the SConstruct pipeline).",
         type=str,
     )
     seqs_args.add_argument(

site_scons/options.py

@@ -152,7 +152,7 @@ def get_options(env):
     user_tag = dataset_tag if dataset_tag else ""
     test_tag = "test" if test_run else ""
     match_indel_in_uid_tag = (
-        "match-indels-in-uid-{}".format(match_indel_in_uid)
+        "match-indel-in-uid-{}".format(match_indel_in_uid)
         if match_indel_in_uid
         else ""
     )