更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。

99.scripts/miscs/check_frameshift.py

@@ -0,0 +1,128 @@
+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Check and process frameshift in alignment files.
+"""
+
+import shutil
+import pandas as pd
+from pathlib import Path
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+from Bio.Seq import Seq
+import sys
+import argparse
+
+
+def parse_frameshift_list(fs_list: Path) -> pd.DataFrame:
+    """
+    Parse a frameshift list file into a pandas DataFrame.
+
+    Args:
+        fs_list (Path): Path to the frameshift list file.
+
+    Returns:
+        pd.DataFrame: DataFrame containing the frameshift information.
+    """
+    try:
+        df = pd.read_csv(fs_list, sep=",", header=0)
+    except Exception as e:
+        print(f"Error reading frameshift list file {fs_list}: {e}")
+        sys.exit(1)
+    return df
+
+
+def get_alignment_files(aln_dir: Path, ext: str) -> list[Path]:
+    """
+    Get a list of alignment files in a directory with a specific extension.
+
+    Args:
+        aln_dir (Path): Path to the directory containing alignment files.
+        ext (str): Extension of the alignment files.
+
+    Returns:
+        list[Path]: List of Paths to the alignment files.
+    """
+    try:
+        aln_files = list(aln_dir.glob(f"*{ext}"))
+    except Exception as e:
+        print(f"Error accessing alignment files in {aln_dir}: {e}")
+        sys.exit(1)
+    return aln_files
+
+
+def main(alignment_dir: str, ext: str, frameshift_list: str, outdir: str):
+    aln_dir = Path(alignment_dir)
+    fs_list_path = Path(frameshift_list)
+    out_dir = Path(outdir)
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    fs_df = parse_frameshift_list(fs_list_path)
+    aln_files = get_alignment_files(aln_dir, ext)
+    good_aln_count = 0
+    keep_fs_count = 0
+    discard_count = 0
+
+    for file in aln_files:
+        if str(file) not in fs_df["alignment_file"].values.tolist():
+            try:
+                shutil.copy(file, out_dir / file.name)
+                good_aln_count += 1
+                continue
+            except Exception as e:
+                print(f"Error copying file {file} to {out_dir}: {e}")
+                sys.exit(1)
+        if (
+            fs_df.loc[
+                fs_df["alignment_file"] == str(file), "possible_attributions"
+            ].values[0]
+            == "Framshift only in Ziziphus jujuba or Elaeagnus pungens"
+        ):
+            try:
+                records = []
+                for record in SeqIO.parse(file, "fasta"):
+                    seq = str(record.seq).replace("!", "-")
+                    id = record.id
+                    records.append(SeqRecord(seq=Seq(seq), id=id, description=""))
+                print(
+                    f"Keep the alignment file with frameshift: {file}. Due to frameshift only in outgroup."
+                )
+                keep_fs_count += 1
+                SeqIO.write(records, out_dir / file.name, "fasta")
+            except Exception as e:
+                print(f"Error processing file {file}: {e}")
+                sys.exit(1)
+        else:
+            discard_count += 1
+    print("Frameshift processing completed successfully.")
+    print(f"Number of good alignments copied: {good_aln_count}")
+    print(f"Number of alignments with frameshift kept: {keep_fs_count}")
+    print(f"Number of alignments with frameshift discarded: {discard_count}")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Check and process frameshift in alignment files."
+    )
+    parser.add_argument(
+        "-a",
+        "--alignment_dir",
+        required=True,
+        help="Directory containing alignment files",
+    )
+    parser.add_argument(
+        "-e", "--ext", default=".nal", help="Extension of alignment files"
+    )
+    parser.add_argument(
+        "-f",
+        "--frameshift_list",
+        required=True,
+        help="CSV file listing frameshift information",
+    )
+    parser.add_argument(
+        "-o", "--outdir", required=True, help="Output directory for processed files"
+    )
+    args = parser.parse_args()
+
+    main(args.alignment_dir, args.ext, args.frameshift_list, args.outdir)