Delete msp_to_mgf.py

msp_to_mgf.py

@@ -1,178 +0,0 @@
-# -*- coding: utf-8 -*-
-import re
-from pathlib import Path
-from openpyxl import Workbook
-
-# =========================================================
-# 1) 路径配置：改这里即可
-#    INPUT_DIR : 你截图里的 extracted 目录（存放 .msp）
-#    OUTPUT_DIR: 输出 .mgf 的目录（会自动创建）
-#    EXCEL_PATH: 输出统计表
-# =========================================================
-INPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Rat/extracted")
-OUTPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Rat/mgf")
-OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
-
-EXCEL_PATH = OUTPUT_DIR / "msp_to_mgf_summary.xlsx"
-
-# 进度打印（大文件可调）
-PROGRESS_EVERY_SPECTRA = 50000
-
-# =========================================================
-# 2) MSP 字段解析函数（保持和你单文件脚本一致）
-# =========================================================
-def parse_sequence_from_name(name_val: str) -> str:
-    # Name: SEQUENCE/charge_...
-    return name_val.split("/", 1)[0].strip()
-
-def parse_charge_from_name(name_val: str):
-    m = re.search(r"/(\d+)", name_val)
-    return int(m.group(1)) if m else None
-
-def parse_mz_exact_from_comment(line: str):
-    # Comment: ... Mz_exact=536.5844 ...
-    m = re.search(r"\bMz_exact=([0-9]*\.?[0-9]+)", line)
-    return float(m.group(1)) if m else None
-
-# =========================================================
-# 3) 转换单个 MSP -> MGF，并返回统计信息
-#    - Spectra count: Num peaks 次数
-#    - Unique peptides: 对 Name: 的 seq 去重（与你单文件脚本一致）
-# =========================================================
-def convert_one_msp(msp_path: Path, mgf_path: Path):
-    spectra_count = 0
-    unique_peptides = set()
-
-    with msp_path.open("r", encoding="utf-8", errors="replace") as fin, \
-         mgf_path.open("w", encoding="utf-8") as fout:
-
-        name_val = None
-        seq = None
-        charge = None
-        mw = None               # 你要求用作 PEPMASS
-        precursor_mz = None     # 仅用于辅助记录（Mz_exact）
-
-        for line in fin:
-            line = line.rstrip("\n")
-
-            if line.startswith("Name:"):
-                name_val = line.split("Name:", 1)[1].strip()
-                seq = parse_sequence_from_name(name_val)
-                charge = parse_charge_from_name(name_val)
-                unique_peptides.add(seq)
-
-            elif line.startswith("MW:"):
-                try:
-                    mw = float(line.split("MW:", 1)[1].strip())
-                except Exception:
-                    mw = None
-
-            elif line.startswith("Comment:"):
-                precursor_mz = parse_mz_exact_from_comment(line)
-
-            elif line.startswith("Num peaks:"):
-                num_peaks = int(line.split("Num peaks:", 1)[1].strip())
-                spectra_count += 1
-
-                # ===== 写一个 MGF block =====
-                fout.write("BEGIN IONS\n")
-
-                if seq is not None and charge is not None:
-                    fout.write(f"TITLE={seq}/z{charge}\n")
-                elif seq is not None:
-                    fout.write(f"TITLE={seq}\n")
-                else:
-                    fout.write(f"TITLE=Spectrum_{spectra_count}\n")
-
-                # 你要求：PEPMASS = MW（不做换算）
-                if mw is not None:
-                    fout.write(f"PEPMASS={mw:.6f}\n")
-
-                if charge is not None:
-                    fout.write(f"CHARGE={charge}+\n")
-
-                # 自定义字段
-                if seq is not None:
-                    fout.write(f"SEQ={seq}\n")
-
-                # 可选：记录 Mz_exact（不影响你要求）
-                if precursor_mz is not None:
-                    fout.write(f"PRECURSOR_MZ={precursor_mz:.6f}\n")
-
-                # 峰：每行 "m/z intensity"
-                for _ in range(num_peaks):
-                    peak_line = next(fin).strip()
-                    if not peak_line:
-                        continue
-                    parts = peak_line.split()
-                    if len(parts) >= 2:
-                        fout.write(f"{parts[0]} {parts[1]}\n")
-
-                fout.write("END IONS\n\n")
-
-                # reset 当前谱状态（与你单文件脚本一致）
-                name_val = None
-                seq = None
-                charge = None
-                mw = None
-                precursor_mz = None
-
-                if spectra_count % PROGRESS_EVERY_SPECTRA == 0:
-                    print(f"  ... {msp_path.name}: spectra={spectra_count}")
-
-    return spectra_count, len(unique_peptides)
-
-# =========================================================
-# 4) 写 Excel（3列：文件名 / Spectra count / Unique peptides）
-# =========================================================
-def write_excel(excel_path: Path, rows):
-    wb = Workbook()
-    ws = wb.active
-    ws.title = "summary"
-
-    for r in rows:
-        ws.append(list(r))
-
-    ws.column_dimensions["A"].width = 55
-    ws.column_dimensions["B"].width = 18
-    ws.column_dimensions["C"].width = 20
-
-    wb.save(excel_path)
-
-# =========================================================
-# 5) 批量处理
-# =========================================================
-def main():
-    if not INPUT_DIR.exists():
-        raise FileNotFoundError(f"INPUT_DIR not found: {INPUT_DIR}")
-
-    msp_files = sorted(INPUT_DIR.glob("*.msp"))
-    if not msp_files:
-        print(f"No .msp files found in: {INPUT_DIR}")
-        return
-
-    print(f"Input dir : {INPUT_DIR}")
-    print(f"Output dir: {OUTPUT_DIR}")
-    print(f"Found {len(msp_files)} MSP files.")
-
-    rows = [("file_name", "spectra_count", "unique_peptides")]
-
-    for idx, msp_path in enumerate(msp_files, 1):
-        mgf_path = OUTPUT_DIR / (msp_path.stem + ".mgf")
-
-        print(f"\n[{idx}/{len(msp_files)}] Converting: {msp_path.name}")
-        spectra_count, unique_pep = convert_one_msp(msp_path, mgf_path)
-
-        print(f"  -> MGF: {mgf_path.name}")
-        print(f"  Spectra count   : {spectra_count}")
-        print(f"  Unique peptides : {unique_pep}")
-
-        rows.append((msp_path.name, spectra_count, unique_pep))
-
-    write_excel(EXCEL_PATH, rows)
-
-    print("\n================= DONE =================")
-    print(f"Excel summary: {EXCEL_PATH}")
-
-if __name__ == "__main__":
-    main()