Delete msp_to_mgf_副本.py

msp_to_mgf_副本.py

@@ -1,130 +0,0 @@
-# -*- coding: utf-8 -*-
-import os
-import re
-
-# =========================================================
-# 1) 读取路径与保存路径（请你按自己的电脑路径修改）
-# =========================================================
-# 示例（macOS）:
-MSP_PATH = "/Users/guanmumu/Desktop/Data/Human/extracted/human_hair_selected_with_GVPs_passed.msp"
-MGF_PATH = "/Users/guanmumu/Desktop/Data/human_hair_selected_with_GVPs_passed.mgf"
-
-# 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
-# =========================================================
-def parse_sequence_from_name(name_val: str) -> str:
-    # Name: SEQUENCE/charge_...
-    return name_val.split("/")[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) 主逻辑：流式读取 MSP，写 MGF
-# =========================================================
-def main():
-    spectra_count = 0
-    unique_peptides = set()
-
-    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
-        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:"):
-                # 进入峰列表块
-                num_peaks = int(line.split("Num peaks:", 1)[1].strip())
-
-                spectra_count += 1
-
-                # ===================== 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:
-                    fout.write(f"TITLE={seq}\n")
-                else:
-                    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")
-
-                # 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")
-
-                # 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")
-
-                # 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:
-                        mz = parts[0]
-                        inten = parts[1]
-                        fout.write(f"{mz} {inten}\n")
-
-                fout.write("END IONS\n\n")
-
-                # reset 当前谱状态
-                name_val = None
-                seq = None
-                charge = None
-                mw = None
-                precursor_mz = None
-
-    # =========================================================
-    # 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()