Update

sai/parsers/score_parser.py

@@ -52,8 +52,6 @@ def _run_score(args: argparse.Namespace) -> None:
             Step size for moving the window along the sequence.
         - num_src : int
             Number of source populations. The length of `args.y` should match `num_src`.
-        - anc_allele_file : str
-            Path to the ancestral allele file.
         - ploidy : int
             Ploidy level of the organism.
         - is_phased : bool
@@ -91,7 +89,6 @@ def _run_score(args: argparse.Namespace) -> None:
         win_len=args.win_len,
         win_step=args.win_step,
         num_src=args.num_src,
-        anc_allele_file=args.anc_alleles,
         ploidy=args.ploidy,
         is_phased=args.is_phased,
         w=args.w,
@@ -168,13 +165,6 @@ def add_score_parser(subparsers: argparse.ArgumentParser) -> None:
         default=1,
         help="number of source populations to include. Default is 1.",
     )
-    parser.add_argument(
-        "--anc-alleles",
-        dest="anc_alleles",
-        type=existed_file,
-        default=None,
-        help="path to the BED file with ancestral allele information. Default is None.",
-    )
     parser.add_argument(
         "--ploidy",
         type=positive_int,

sai/sai.py

@@ -34,7 +34,6 @@ def score(
     win_len: int,
     win_step: int,
     num_src: int,
-    anc_allele_file: str,
     ploidy: int,
     is_phased: bool,
     w: float,
@@ -65,8 +64,6 @@ def score(
         Step size in base pairs between consecutive windows.
     num_src : int
         Number of source populations to include in each windowed analysis.
-    anc_allele_file : str
-        Path to the file containing ancestral allele information.
     ploidy : int
         The ploidy level of the genome.
     is_phased : bool
@@ -93,7 +90,6 @@ def score(
         win_len=win_len,
         win_step=win_step,
         num_src=num_src,
-        anc_allele_file=anc_allele_file,
         ploidy=ploidy,
         is_phased=is_phased,
     )

sai/utils/generators/WindowDataGenerator.py

@@ -39,7 +39,6 @@ def __init__(
         win_len: int,
         win_step: int,
         num_src: int = 1,
-        anc_allele_file: str = None,
         ploidy: int = 2,
         is_phased: bool = True,
     ):
@@ -110,7 +109,7 @@ def __init__(
             ref_ind_file=ref_ind_file,
             tgt_ind_file=tgt_ind_file,
             src_ind_file=src_ind_file,
-            anc_allele_file=anc_allele_file,
+            anc_allele_file=None,
             is_phased=is_phased,
             filter_ref=False,
             filter_tgt=False,

tests/parsers/test_score_parser.py

@@ -53,8 +53,6 @@ def test_add_score_parser(parser):
             "10000",
             "--num-src",
             "2",
-            "--anc-alleles",
-            "tests/data/test.anc.allele.bed",
             "--ploidy",
             "2",
             "--phased",
@@ -84,7 +82,6 @@ def test_add_score_parser(parser):
     assert args.win_len == 50000
     assert args.win_step == 10000
     assert args.num_src == 2
-    assert args.anc_alleles == "tests/data/test.anc.allele.bed"
     assert args.ploidy == 2
     assert args.is_phased is True
     assert args.w == 0.3

tests/test_sai.py

@@ -55,7 +55,6 @@ def test_score(example_data, capfd):
         win_len=6666,
         win_step=6666,
         num_src=1,
-        anc_allele_file=None,
         ploidy=2,
         is_phased=True,
         w=0.3,
@@ -89,7 +88,6 @@ def test_outlier(example_data):
         win_len=6666,
         win_step=6666,
         num_src=1,
-        anc_allele_file=None,
         ploidy=2,
         is_phased=True,
         w=0.3,

tests/utils/generators/test_WindowDataGenerator.py

@@ -33,7 +33,6 @@ def test_generator():
         src_ind_file="tests/data/test.src.ind.list",
         win_len=1000,  # Set window length as appropriate for testing
         win_step=500,  # Set window step as appropriate for testing
-        anc_allele_file=None,
         ploidy=2,
         is_phased=True,
     )
@@ -86,7 +85,6 @@ def test_generator_two_sources():
         win_len=1000,  # Set window length as appropriate for testing
         win_step=500,  # Set window step as appropriate for testing
         num_src=2,  # Set to 2 to test two-source combinations
-        anc_allele_file=None,
         ploidy=2,
         is_phased=False,
     )