adding main batch hits

CNuge · Mar 11, 2020 · 504b0a9 · 504b0a9
1 parent e31aedf
commit 504b0a9
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diff --git a/alfie/tests/__pycache__/test_script.cpython-37-pytest-5.2.1.pyc b/alfie/tests/__pycache__/test_script.cpython-37-pytest-5.2.1.pyc
diff --git a/alfie/tests/__pycache__/test_seqio.cpython-37-pytest-5.2.1.pyc b/alfie/tests/__pycache__/test_seqio.cpython-37-pytest-5.2.1.pyc
diff --git a/alfie/tests/test_script.py b/alfie/tests/test_script.py
@@ -57,6 +57,26 @@ def test_main_with_args():
 		os.remove("alfie_out/"+x)
 	os.rmdir("alfie_out")
 
+
+	#batch process a fasta file
+	sys.argv = ['alfie', "-f", ex_fasta_file, "-b", "20"]
+	alf.main()
+
+	fasta_main_outputs = ['animalia_example_data.fasta',
+							'bacteria_example_data.fasta',
+							'fungi_example_data.fasta',		 
+							'plantae_example_data.fasta',
+							'protista_example_data.fasta']
+
+	#check outputs were made
+	assert sorted(os.listdir('alfie_out')) == fasta_main_outputs
+	#tear down the outputs
+	for x in fasta_main_outputs:
+		os.remove("alfie_out/"+x)
+	os.rmdir("alfie_out")
+
+
+
 	#process a fastq file
 	sys.argv = ['alfie', "-f", ex_fastq_file]
 	alf.main()
@@ -73,3 +93,20 @@ def test_main_with_args():
 	for x in fastq_main_outputs:
 		os.remove("alfie_out/"+x)
 	os.rmdir("alfie_out")
+
+	#batch process a fastq file
+	sys.argv = ['alfie', "-f", ex_fastq_file, "-b", "20"]
+	alf.main()
+
+	fastq_main_outputs = ['animalia_example_data.fastq',
+							'bacteria_example_data.fastq',
+							'fungi_example_data.fastq',
+							'plantae_example_data.fastq',
+							'protista_example_data.fastq']
+
+	#check for outputs
+	assert sorted(os.listdir('alfie_out')) == fastq_main_outputs
+
+	for x in fastq_main_outputs:
+		os.remove("alfie_out/"+x)
+	os.rmdir("alfie_out")