Added STEC O157:H7 GCA_000181775.1 gzip compressed for testing

phac-nml · Jul 22, 2024 · 58b956e · 58b956e
1 parent 33eac5d
commit 58b956e
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Showing 3 changed files with 2 additions and 1 deletion.
diff --git a/ectyper/speciesIdentification.py b/ectyper/speciesIdentification.py
@@ -305,7 +305,7 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
 
     for bf in ofiles:
         sampleName = getSampleName(bf)
-        LOG.warning("Non fasta / fastq file.")
+        LOG.warning(f"{sampleName} is non fasta / fastq file. Species identification aborted")
         other_files_dict[sampleName] = {"error":"Non fasta / fastq file. ","filepath":bf,"species":"-"}
 
     for file in filesnotfound:

diff --git a/test/Data/test_dir/GCA_000181775.1_ASM18177v1_genomic.fna.gz b/test/Data/test_dir/GCA_000181775.1_ASM18177v1_genomic.fna.gz
diff --git a/test/test_ectyper_integration.py b/test/test_ectyper_integration.py
@@ -143,6 +143,7 @@ def test_multiple_directories(caplog):
     assert any([True if re.match(r".+sample.fasta.+WARNING\s+\(WRONG\s+SPECIES\).+Non fasta / fastq file", line) else False for line in caplog.text.splitlines()]), "Issue with sample.fasta"
     assert any([True if re.match(r".+sampletar.+WARNING\s+\(WRONG\s+SPECIES\).+Non fasta / fastq file", line) else False for line in caplog.text.splitlines()]), "Issue with sampletar"
     assert any([True if re.match(r".+test_junk.+WARNING\s+\(WRONG\s+SPECIES\).+Non fasta / fastq file", line) else False for line in caplog.text.splitlines()]), "Issue with test_junk"
+    assert any([True if re.match(r".+GCA_000181775\.1_ASM18177v1_genomic\s+Escherichia\s+coli\s+O157\s+H7.+REPORTABLE", line) else False for line in caplog.text.splitlines()]), "Issue with GCF_000181775.1_ASM18177v1"
 
 
 def test_mash_sketch_and_assembly_metadata(tmpdir):