added c3 trimming

clipkit/args_processing.py

@@ -36,6 +36,12 @@ def process_args(args) -> dict:
     quiet = args.quiet or False
     sequence_type = SeqType(args.sequence_type.lower()) if args.sequence_type else None
 
+    if codon and mode == TrimmingMode.c3:
+        logger.warning(
+            "C3 and codon-based trimming are incompatible.\nCodon-based trimming removes whole codons while C3 removes every third codon position."
+        )
+        sys.exit()
+
     return dict(
         input_file=input_file,
         output_file=output_file,

clipkit/modes.py

@@ -16,3 +16,4 @@ class TrimmingMode(Enum):
     kpic = "kpic"
     kpic_gappy = "kpic-gappy"
     kpic_smart_gap = "kpic-smart-gap"
+    c3 = "c3"

clipkit/msa.py

@@ -209,9 +209,12 @@ def determine_site_positions_to_trim(self, mode, gap_threshold, codon=False):
                     (sites_to_trim_gaps_based, sites_to_trim_classification_based)
                 )
             )
-
-        if codon:
+        elif mode == TrimmingMode.c3:
+            sites_to_trim = np.arange(3, self._original_length + 1, 3) - 1
+        if codon and mode != TrimmingMode.c3:
             """
+            NOTE: ignoring c3 mode otherwise we would ALWAYS trim the entire file by definition.
+
             For each position in sites_to_trim we need the full triplet of codon positions tuple.
             Example:
                 [2, 9] -> [1, 2, 3, 7, 8, 9]
@@ -258,8 +261,8 @@ def determine_codon_triplet_positions(self, alignment_position):
 
         We filter to make sure we are not including any positions out of range
         """
-        block = alignment_position // 3
-        codon_triplet_index_start = block * 3
+        block = alignment_position // self._codon_size
+        codon_triplet_index_start = block * self._codon_size
         sites = [
             codon_triplet_index_start,
             codon_triplet_index_start + 1,

clipkit/parser.py

@@ -73,7 +73,8 @@ def create_parser() -> ArgumentParser:
                     kpic-gappy,                
                     kpi,
                     kpi-smart-gap,
-                    kpi-gappy>                      
+                    kpi-gappy,
+                    c3>                      
                                                     
         -g, --gaps <threshold_of_gaps>              specifies gaps threshold
                                                     (default: 0.9)
@@ -116,6 +117,7 @@ def create_parser() -> ArgumentParser:
             kpi: keep only parsimony informative sites
             kpi-smart-gap: a combination of kpi- and smart-gap-based trimming
             kpi-gappy: a combination of kpi- and gappy-based trimming
+            c3: remove every third codon position
 
         Gaps
             Positions with gappyness greater than threshold will be trimmed. 

clipkit/version.py

@@ -1 +1 @@
-__version__ = "2.1.3"
+__version__ = "2.2.0"

tests/integration/expected/simple.fa_c3

@@ -0,0 +1,10 @@
+>1
+A-TA
+>2
+A--A
+>3
+A--T
+>4
+AG-T
+>5
+AC-T

tests/integration/samples/simple.fa.out

@@ -0,0 +1,10 @@
+>1
+A-TA
+>2
+A--A
+>3
+A--T
+>4
+AG-T
+>5
+AC-T

tests/integration/test_c3.py

@@ -0,0 +1,44 @@
+import pytest
+from pathlib import Path
+
+from clipkit.clipkit import execute
+from clipkit.files import FileFormat
+from clipkit.modes import TrimmingMode
+from clipkit.settings import DEFAULT_AA_GAP_CHARS, DEFAULT_NT_GAP_CHARS
+
+here = Path(__file__)
+
+
+@pytest.mark.integration
+class TestC3Out(object):
+    def test_simple_c3(self):
+        """
+        test codon
+        usage: clipkit simple.fa c3
+        """
+        output_file = "output/simple.fa_c3"
+
+        kwargs = dict(
+            input_file=f"{here.parent}/samples/simple.fa",
+            output_file=output_file,
+            input_file_format="fasta",
+            output_file_format="fasta",
+            sequence_type=None,
+            complement=False,
+            codon=False,
+            gaps=None,
+            mode=TrimmingMode.c3,
+            use_log=False,
+            gap_characters=DEFAULT_NT_GAP_CHARS,
+            quiet=True,
+        )
+
+        execute(**kwargs)
+
+        with open(f"{here.parent}/expected/simple.fa_c3", "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

tests/unit/test_args_parsing.py

@@ -110,3 +110,9 @@ def test_process_args_expected_keywords(self, args):
             "quiet",
         ]
         assert sorted(res.keys()) == sorted(expected_keys)
+
+    def test_incompatible_codon_args(self, args):
+        args.codon = True
+        args.mode = TrimmingMode.c3
+        with pytest.raises(SystemExit):
+            process_args(args)