--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/tests/integration/test_writing_to_log_file.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,128 @@
+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 TestOutLog(object):
+    def test_simple(self):
+        """
+        test output in clustal format
+        usage: clipkit simple.fa -l
+        """
+        input_file = f"{here.parent}/samples/simple.fa"
+        output_file = "output/simple.fa.clipkit"
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=True,
+        )
+        execute(**kwargs)
+
+        with open(f"{here.parent}/expected/simple.fa.clipkit.log", "r") as expected:
+            expected_content = expected.read()
+
+        with open(f"{output_file}.log", "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_simple_long_description(self):
+        """
+        test output in clustal format
+        usage: clipkit simple_long_description.fa -l
+        """
+        input_file = f"{here.parent}/samples/simple_long_description.fa"
+        output_file = "output/simple_long_description.fa.clipkit"
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=True,
+        )
+        execute(**kwargs)
+
+        with open(f"{here.parent}/expected/simple_long_description.fa.clipkit.log", "r") as expected:
+            expected_content = expected.read()
+
+        with open(f"{output_file}.log", "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_12_YIL115C_Anc_2_253_codon_aln(self):
+        """
+        test output in clustal format
+        usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -l
+        """
+        input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
+        output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit"
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=True,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log",
+            "r",
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(f"{output_file}.log", "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_EOG091N44M8_nt(self):
+        """
+        test output in clustal format
+        usage: clipkit EOG091N44M8_nt.fa -l
+        """
+        input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
+        output_file = "output/EOG091N44M8_nt.fa.clipkit"
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9,
+            mode=TrimmingMode.gappy,
+            use_log=True,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/EOG091N44M8_nt.fa.clipkit.log", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(f"{output_file}.log", "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content