mgnify-pipelines-toolkit 1.0.7__tar.gz → 1.0.9__tar.gz

{mgnify_pipelines_toolkit-1.0.7 → mgnify_pipelines_toolkit-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.7
+Version: 1.0.9
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0

{mgnify_pipelines_toolkit-1.0.7 → mgnify_pipelines_toolkit-1.0.9}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py

@@ -401,12 +401,10 @@ def retrieve_regions(
         region_counter = defaultdict(int)
 
         regions_to_remove = []
-
         for model, value in multiregion_matches.items():
             marker_gene = determine_marker_gene(determine_domain(model))
             for region in value:
                 region_counter[f"{marker_gene}.{region}"] += 1
-
         for region, count in region_counter.items():
             if count < MIN_SEQ_COUNT:
                 regions_to_remove.append(region)
@@ -421,12 +419,16 @@ def retrieve_regions(
         for model, value in multiregion_matches.items():
             new_value = []
             for region in value:
+                if region == "":
+                    continue
                 marker_gene = determine_marker_gene(determine_domain(model))
                 full_region = f"{marker_gene}.{region}"
                 if full_region not in regions_to_remove:
                     new_value.append(region)
             if not new_value:
                 models_to_remove.append(model)
+            if len(new_value) < MIN_SEQ_COUNT:
+                models_to_remove.append(model)
             multiregion_matches[model] = new_value
 
         [multiregion_matches.pop(model) for model in models_to_remove]
@@ -463,6 +465,9 @@ def retrieve_regions(
             for key, value in temp_seq_counter.items():
                 seq_per_variable_region_count.setdefault(key, 0)
                 seq_per_variable_region_count[key] += value
+        else:
+            logging.info("No output will be produced - the run is ambiguous.")
+            continue
 
     json_outfile = "{}.json".format(outfile_prefix)
     tsv_outfile = "{}.tsv".format(outfile_prefix)

{mgnify_pipelines_toolkit-1.0.7 → mgnify_pipelines_toolkit-1.0.9}/mgnify_pipelines_toolkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.7
+Version: 1.0.9
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0

{mgnify_pipelines_toolkit-1.0.7 → mgnify_pipelines_toolkit-1.0.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mgnify_pipelines_toolkit"
-version = "1.0.7"
+version = "1.0.9"
 readme = "README.md"
 license = {text = "Apache Software License 2.0"}
 authors = [