Fixed pytest small error with test_emtpy_BLAST_antigen_hits

phac-nml · Jul 30, 2024 · 4ef8526 · 4ef8526
1 parent 22b6a98
commit 4ef8526
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/ectyper/ectyper.py b/ectyper/ectyper.py
@@ -196,7 +196,7 @@ def run_program():
     # Add empty rows for genomes without a blast result or non-E.coli samples that did not undergo typing
     final_predictions = predictionFunctions.add_non_predicted(
         raw_genome_files, predictions_dict, other_genomes_dict, filesnotfound_dict, ecoli_genomes_dict)
-    print(final_predictions)
+
 
     for sample in final_predictions.keys():
         final_predictions[sample]["database"] = "v"+ectyperdb_dict["version"] + " (" + ectyperdb_dict["date"] + ")"

diff --git a/ectyper/predictionFunctions.py b/ectyper/predictionFunctions.py
@@ -221,11 +221,17 @@ def predict_pathotype_and_shiga_toxin_subtype(ecoli_genome_files_dict, other_gen
             "-out", f"{temp_dir}/blast_pathotype_result.txt",
             "-outfmt", "6 qseqid qlen sseqid length pident sstart send sframe slen qcovhsp bitscore sseq"
         ]
-        LOG.debug(f"BLASTN results on pathotype database written to {temp_dir}/blast_pathotype_result.txt ...")
-        cmd_status = subprocess_util.run_subprocess(cmd)
 
+        cmd_status = subprocess_util.run_subprocess(cmd)
+        if cmd_status.returncode == 0:
+            LOG.info(f"BLASTN on pathotype database for {g} was successful and results written to {temp_dir}/blast_pathotype_result.txt ...")
+        else:
+            LOG.critical(f"BLASTn against pathotype database failed with error code {cmd_status.returncode} and pathotype results for {g} would NOT be available. Skipping pathotyping ...")
+            continue
+
+
         if os.stat(f'{temp_dir}/blast_pathotype_result.txt').st_size == 0:
-            LOG.warning(f"No pathotype signatures found for sample {g} as pathotype BLAST results file {temp_dir}/blast_pathotype_result.txt is empty. Skipping ...")
+            LOG.warning(f"No pathotype signatures found for sample {g} as pathotype BLAST results file {temp_dir}/blast_pathotype_result.txt is empty. Skipping pathotyping...")
             predictions_pathotype_dict[g]={field:'-' for field in definitions.PATHOTYPE_TOXIN_FIELDS}
             predictions_pathotype_dict[g]['pathotype']= ['ND']
             continue

diff --git a/test/test_complex_inputs.py b/test/test_complex_inputs.py
@@ -52,7 +52,7 @@ def test_emtpy_BLAST_antigen_hits(tmpdir):
     with open(file=ectyper.definitions.SEROTYPE_ALLELE_JSON) as fp:
             ectyperdb_dict = json.load(fp)
     alleles_fasta_file = ectyper.create_alleles_fasta_file(tmpdir, ectyperdb_dict)
-    db_prediction_dict = ectyper.genome_group_prediction([args.input], alleles_fasta_file, args, tmpdir, ectyperdb_dict)
+    db_prediction_dict = ectyper.genome_group_prediction(args.input, alleles_fasta_file, args, tmpdir, ectyperdb_dict)
     assert db_prediction_dict == {}
 
 def test_invalid_fasta():