MRG: make a clear error when acc cannot be found (#23)

* MRG: make a clear error when acc cannot be found

* bump v

* upd

* refactor

Author: ctb

pyproject.toml

@@ -3,7 +3,7 @@ name = "sourmash_plugin_pangenomics"
 description = "sourmash plugin to do pangenomics."
 readme = "README.md"
 requires-python = ">=3.11"
-version = "0.3.0"
+version = "0.3.1"
 authors = [
   {name = "Colton Baumler", email = "ccbaumler@ucdavis.edu"},
   {name = "Titus Brown", email = "titus@idyll.org"},

src/sourmash_plugin_pangenomics.py

@@ -13,6 +13,7 @@
 import os
 import re
 import pprint
+from difflib import get_close_matches
 
 import sourmash
 import sourmash_utils
@@ -222,23 +223,27 @@ def pangenome_createdb_main(args):
             ident = tax_utils.get_ident(name)
 
             # grab relevant lineage name
-            try:
-                lineage_tup = taxdb[ident]
-            except KeyError:  # older versions of genbank are not named with version!
-                try:
-                    if "." in ident:
-                        short_ident = ident.split(".")[0]
-                        lineage_tup = taxdb[short_ident]
-                    else:
-                        for i in range(1, 10):
-                            try:
-                                new_ident = f"{ident}.{i}"
-                                lineage_tup = taxdb[new_ident]
-                                break
-                            except KeyError:
-                                continue
-                except:
-                    print("Wow, that sucks!")
+            lineage_tup = taxdb.get(ident)
+
+            # not found and has a .? maybe we can strip off the version.
+            if lineage_tup is None and "." in ident:
+                short_ident = ident.split(".")[0]
+                lineage_tup = taxdb.get(ident)
+
+            # not found and has no .? Try many versions.
+            if lineage_tup is None and "." not in ident:
+                for i in range(1, 10):
+                    new_ident = f"{ident}.{i}"
+                    lineage_tup = taxdb.get(new_ident)
+                    if lineage_tup is not None:
+                        break
+
+            if lineage_tup is None:
+                print(f"cannot find ident {ident} in the provided taxonomy ifle.")
+                print(f"The three closest matches to {ident} are:")
+                for k in get_close_matches(ident, taxdb):
+                    print(f"* '{k}'")
+                sys.exit(-1)
 
             lineage_tup = tax_utils.RankLineageInfo(lineage=lineage_tup)
             lineage_pair = lineage_tup.lineage_at_rank(args.rank)