mgnify-pipelines-toolkit 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

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.dist-info → mgnify_pipelines_toolkit-1.0.9.dist-info}/METADATA

@@ -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.dist-info → mgnify_pipelines_toolkit-1.0.9.dist-info}/RECORD

@@ -4,7 +4,7 @@ mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py,sha256=8qmb57E2XBrw
 mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py,sha256=2-URxvcl13_8O9bUmoa3-KMPSvdTaLbxfFDY-ycs_4M,5316
 mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py,sha256=cRoHPM-VB_L3NWYgkNWuyzqIqhzwHJuU3-6BiiS2lnw,7553
 mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py,sha256=RAdqakH05Qt_LG9jlV7P2M90o5KmlAXmDFQ4X51NIBE,5387
-mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=EqfaATb5agvtQOhJqrb2YS6OxtCXvxC-q_05UzvDYug,19926
+mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=7QG7wiExTHT_gCxIF2ZwcXKzQo_lG-kgWsa6l8czq0s,20194
 mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py,sha256=vC3nKxggnSljfw4HNkugXbXfGvLx7XnryEE7eEGqfqs,3552
 mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=soTewFddtebW-EcejGh9whs3cBLWJrGCYdPc0KukoAw,8756
 mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py,sha256=BLqhflblUegCvuQic16PrFXfIXlFWmGkmWJyl4wJoLQ,5040
@@ -48,9 +48,9 @@ mgnify_pipelines_toolkit/schemas/schemas.py,sha256=pnH8LUH8i2ACNvFNWyG-n-eIHZcI5
 mgnify_pipelines_toolkit/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mgnify_pipelines_toolkit/utils/fasta_to_delimited.py,sha256=lgYIR1S4crURY7C7nFtgE6QMV4u4zCNsUrVkcRnsEEo,3996
 mgnify_pipelines_toolkit/utils/get_mpt_version.py,sha256=aS9bWrC9CP7tpxoEVg6eEYt18-pmjG7fJl5Mchz4YOU,798
-mgnify_pipelines_toolkit-1.0.7.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mgnify_pipelines_toolkit-1.0.7.dist-info/METADATA,sha256=I4UE0FbUbMqhttDW5WK7TthTY26aeqr4IDvYYBX1Wag,5810
-mgnify_pipelines_toolkit-1.0.7.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
-mgnify_pipelines_toolkit-1.0.7.dist-info/entry_points.txt,sha256=T8soGT2to8c_qafw-0itqCn4sjOnxlfaNWHIaHz4H54,3416
-mgnify_pipelines_toolkit-1.0.7.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
-mgnify_pipelines_toolkit-1.0.7.dist-info/RECORD,,
+mgnify_pipelines_toolkit-1.0.9.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mgnify_pipelines_toolkit-1.0.9.dist-info/METADATA,sha256=tgmhTdSfI8calTQZDZXbFSRkdsDludBpzYG0MOF4Mus,5810
+mgnify_pipelines_toolkit-1.0.9.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+mgnify_pipelines_toolkit-1.0.9.dist-info/entry_points.txt,sha256=T8soGT2to8c_qafw-0itqCn4sjOnxlfaNWHIaHz4H54,3416
+mgnify_pipelines_toolkit-1.0.9.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
+mgnify_pipelines_toolkit-1.0.9.dist-info/RECORD,,

{mgnify_pipelines_toolkit-1.0.7.dist-info → mgnify_pipelines_toolkit-1.0.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (79.0.0)
+Generator: setuptools (80.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any