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2011_04_01_bsa_consensus_final_true_lib.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2156f4d7848a698337f933d8600b47a88e1bae6e567c208aa2b62ddc50fbe6d0
+size 949605

msp_to_mgf.py

@@ -1,29 +1,25 @@
 # -*- coding: utf-8 -*-
+import os
 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
+# 1) 读取路径与保存路径（请你按自己的电脑路径修改）
 # =========================================================
-INPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Human/extracted")
-OUTPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Human/mgf")
-OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+# 示例（macOS）:
+MSP_PATH = "/Users/guanmumu/Desktop/Data/BSA/bsa_consensus_final_true_lib.msp"
+MGF_PATH = "/Users/guanmumu/Desktop/Data/BSA/bsa_consensus_final_true_lib.mgf"
 
-EXCEL_PATH = OUTPUT_DIR / "msp_to_mgf_summary.xlsx"
-
-# 进度打印（大文件可调）
-PROGRESS_EVERY_SPECTRA = 50000
+# 如果你想让脚本“放哪儿都能跑”，可以用脚本所在目录：
+# BASE_DIR = os.path.dirname(os.path.abspath(__file__))
+# MSP_PATH = os.path.join(BASE_DIR, "bsa_consensus_final_true_lib.msp")
+# MGF_PATH = os.path.join(BASE_DIR, "bsa_consensus_final_true_lib.pepmass_is_mw.mgf")
 
 # =========================================================
-# 2) MSP 字段解析函数（保持和你单文件脚本一致）
+# 2) MSP 字段解析函数
 # =========================================================
 def parse_sequence_from_name(name_val: str) -> str:
     # Name: SEQUENCE/charge_...
-    return name_val.split("/", 1)[0].strip()
+    return name_val.split("/")[0].strip()
 
 def parse_charge_from_name(name_val: str):
     m = re.search(r"/(\d+)", name_val)
@@ -35,16 +31,14 @@ def parse_mz_exact_from_comment(line: str):
     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）
+# 3) 主逻辑：流式读取 MSP，写 MGF
 # =========================================================
-def convert_one_msp(msp_path: Path, mgf_path: Path):
+def main():
     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:
+    with open(MSP_PATH, "r", encoding="utf-8", errors="replace") as fin, \
+         open(MGF_PATH, "w", encoding="utf-8") as fout:
 
         name_val = None
         seq = None
@@ -71,12 +65,15 @@ def convert_one_msp(msp_path: Path, mgf_path: Path):
                 precursor_mz = parse_mz_exact_from_comment(line)
 
             elif line.startswith("Num peaks:"):
+                # 进入峰列表块
                 num_peaks = int(line.split("Num peaks:", 1)[1].strip())
+
                 spectra_count += 1
 
-                # ===== 写一个 MGF block =====
+                # ===================== 写一个 MGF block =====================
                 fout.write("BEGIN IONS\n")
 
+                # TITLE：建议写得可追溯
                 if seq is not None and charge is not None:
                     fout.write(f"TITLE={seq}/z{charge}\n")
                 elif seq is not None:
@@ -85,94 +82,49 @@ def convert_one_msp(msp_path: Path, mgf_path: Path):
                     fout.write(f"TITLE=Spectrum_{spectra_count}\n")
 
                 # 你要求：PEPMASS = MW（不做换算）
+                # 注意：如果 mw 缺失，会跳过 PEPMASS 行
                 if mw is not None:
                     fout.write(f"PEPMASS={mw:.6f}\n")
 
+                # 电荷
                 if charge is not None:
                     fout.write(f"CHARGE={charge}+\n")
 
-                # 自定义字段
+                # 你要的 sequence 列：这里写在 MGF 自定义字段中
                 if seq is not None:
                     fout.write(f"SEQ={seq}\n")
 
-                # 可选：记录 Mz_exact（不影响你要求）
+                # 辅助字段：把 Comment 里 Mz_exact 也记录下来（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"
+                # 写峰：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")
+                        mz = parts[0]
+                        inten = parts[1]
+                        fout.write(f"{mz} {inten}\n")
 
                 fout.write("END IONS\n\n")
 
-                # reset 当前谱状态（与你单文件脚本一致）
+                # reset 当前谱状态
                 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}")
+    # =========================================================
+    # 4) 最终统计输出
+    # =========================================================
+    print(f"[DONE] MSP input : {MSP_PATH}")
+    print(f"[DONE] MGF output: {MGF_PATH}")
+    print(f"Spectra count      : {spectra_count}")
+    print(f"Unique peptides    : {len(unique_peptides)}")
 
 if __name__ == "__main__":
     main()