--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/tests/integration/test_complementary_output.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,134 @@
+import pytest
+from pathlib import Path
+
+from clipkit.clipkit import execute
+from clipkit.files import FileFormat
+from clipkit.modes import TrimmingMode
+
+here = Path(__file__)
+
+
+@pytest.mark.integration
+class TestComplementOut(object):
+    def test_simple_complement(self):
+        """
+        test complementary output file with a simple case
+        usage: clipkit simple.fa -c
+        """
+        output_file = "output/simple.fa_gappy"
+        complement_out_file = f"{output_file}.complement"
+
+        kwargs = dict(
+            input_file=f"{here.parent}/samples/simple.fa",
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=True,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=False,
+        )
+
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/simple.fa_gappy.complement", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(complement_out_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_simple_long_description_complement(self):
+        """
+        test complementary output file with a simple case
+        usage: clipkit simple_long_description.fa -c
+        """
+        output_file = "output/simple_long_description.fa_gappy"
+        complement_out_file = f"{output_file}.complement"
+
+        kwargs = dict(
+            input_file=f"{here.parent}/samples/simple_long_description.fa",
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=True,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=False,
+        )
+
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/simple_long_description.fa_gappy.complement", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(complement_out_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_12_YIL115C_Anc_2_253_aa_aln_complement(self):
+        """
+        test complementary output file for amino acid yeast sequences
+        usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta -c
+        """
+        output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta_gappy"
+        complement_out_file = f"{output_file}.complement"
+
+        kwargs = dict(
+            input_file=f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta",
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=True,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.fasta_gappy.complement",
+            "r",
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(complement_out_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_EOG091N44M8_aa_complement(self):
+        """
+        test complementary output file for amino acid Penicillium sequences
+        usage: clipkit EOG091N44M8_aa.fa -c
+        """
+        output_file = "output/EOG091N44M8_aa.fa_gappy"
+        complement_out_file = f"{output_file}.complement"
+
+        kwargs = dict(
+            input_file=f"{here.parent}/samples/EOG091N44M8_aa.fa",
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=True,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/EOG091N44M8_aa.fa_gappy.complement", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(complement_out_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content