--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/tests/integration/test_kpic_smart_gap_mode.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,288 @@
+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 TestKPICSmartGapsMode(object):
+    def test_simple_no_change(self):
+        """
+        usage: clipkit simple.fa -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/simple.fa"
+        output_file = "output/simple.fa_smart_gaps"
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.8,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/simple.fa_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_simple_no_change(self):
+        """
+        usage: clipkit simple_long_description.fa -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/simple_long_description.fa"
+        output_file = "output/simple_long_description.fa_kpic_smart_gaps"
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.8,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/simple_long_description.fa_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "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 gappy with codon alignment of yeast sequences
+        usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -m kpic-smart-gap
+        """
+        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_kpic_smart_gaps"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9167,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.clipkit_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_12_YIL115C_Anc_2_253_aa_aln(self):
+        """
+        test gappy with amino acid alignment of yeast sequences
+        usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta  -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta"
+        output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta.clipkit_smart_gaps"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9167,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.clipkit_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_24_ENSG00000163519_aa_aln(self):
+        """
+        test gappy with amino acid alignment of mammalian sequences
+        usage: clipkit 24_ENSG00000163519_aa_aln.fasta  -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/24_ENSG00000163519_aa_aln.fasta"
+        output_file = "output/24_ENSG00000163519_aa_aln.fasta.clipkit"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9583,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/24_ENSG00000163519_aa_aln.clipkit_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_24_ENSG00000163519_codon_aln(self):
+        """
+        test gappy with codon alignment of mammalian sequences
+        usage: clipkit 24_ENSG00000163519_codon_aln.fasta -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
+        output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9583,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/24_ENSG00000163519_codon_aln.clipkit_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_EOG091N44M8_aa(self):
+        """
+        test gappy with amino acid alignment of Penicillium sequences
+        usage: clipkit EOG091N44M8_aa.fa -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/EOG091N44M8_aa.fa"
+        output_file = "output/EOG091N44M8_aa.fa.clipkit"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.8803,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(f"{here.parent}/expected/EOG091N44M8_aa.clipkit_kpic_smart_gaps", "r") as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    def test_EOG091N44M8_nt(self):
+        """
+        test gappy with nucleotide alignment of Penicillium sequences
+        usage: clipkit EOG091N44M8_nt.fa -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
+        output_file = "output/EOG091N44M8_nt.fa.clipkit"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.8803,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(f"{here.parent}/expected/EOG091N44M8_nt.clipkit_kpic_smart_gaps", "r") as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content
+
+    @pytest.mark.slow
+    def test_EOG092C4VOX_aa(self):
+        """
+        test gappy with amino alignment of fungal sequences
+        usage: clipkit EOG092C4VOX_aa_aln.fasta -m kpic-smart-gap
+        """
+        input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
+        output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
+        in_file_format = 'fasta'
+        out_file_format = 'fasta'
+
+        kwargs = dict(
+            input_file=input_file,
+            output_file=output_file,
+            input_file_format='fasta',
+            output_file_format='fasta',
+            complement=False,
+            gaps=0.9993,
+            mode=TrimmingMode.kpic_smart_gap,
+            use_log=False,
+        )
+        execute(**kwargs)
+
+        with open(
+            f"{here.parent}/expected/EOG092C4VOX_aa_aln.clipkit_kpic_smart_gaps", "r"
+        ) as expected:
+            expected_content = expected.read()
+
+        with open(output_file, "r") as out_file:
+            output_content = out_file.read()
+
+        assert expected_content == output_content