Merge pull request #176 from dib-lab/ctb/update_sourmash_411

[MRG] update to sourmash v4.1.1

charcoal/compare_taxonomy.py

@@ -124,9 +124,7 @@ def get_genome_taxonomy(matches_filename, genome_sig_filename, provided_lineage,
                         tax_assign, match_rank, min_f_ident, min_f_major):
     try:
         siglist = list(sourmash.load_file_as_signatures(matches_filename))
-    # TR for empty signatures; update when sourmash#1537 is fixed. 
-    # TR AssertionError covers "assert db" from sourmash _load_database() in sourmash_args.py
-    except (IndexError, AssertionError) as e:
+    except (ValueError, AssertionError) as e:
         siglist = None
 
     if not siglist:

charcoal/contigs_list_contaminants.py

@@ -84,8 +84,7 @@ def main(args):
     # load all of the matches from search --containment in the database
     try:
         siglist = list(sourmash.load_file_as_signatures(args.matches_sig))
-    # TR for empty signatures; update when sourmash#1537 is fixed. 
-    except IndexError:
+    except ValueError:
         siglist = []
     print(f"loaded {len(siglist)} matches from '{args.matches_sig}'")
 

charcoal/contigs_search_taxonomy.py

@@ -32,12 +32,9 @@ def main(args):
     genome_sig = sourmash.load_one_signature(args.genome_sig)
 
     # load all of the matches from search --containment in the database
-    #with open(args.matches_sig, 'rt') as fp:
     try:
         siglist = list(sourmash.load_file_as_signatures(args.matches_sig))
-    # TR for cases with empty sigs that return IndexError; update when sourmash#1537 is fixed
-    # TR AssertionError covers "assert db" from sourmash _load_database() in sourmash_args.py
-    except (IndexError, AssertionError) as e:
+    except (ValueError, AssertionError) as e:
         siglist = []
     print(f"loaded {len(siglist)} matches from '{args.matches_sig}'")
 

charcoal/utils.py

@@ -146,10 +146,7 @@ def close(self):
 
 def gather_at_rank(mh, lca_db, lin_db, match_rank):
     "Run gather, and aggregate at given rank."
-    import copy
-    # needed for sourmash 4.1.1, instead of copy.copy:
-    #minhash = mh.to_mutable()
-    minhash = copy.copy(mh)
+    minhash = mh.to_mutable()
     query_sig = sourmash.SourmashSignature(minhash)
 
     # do the gather: