Delete count.py

count.py

@@ -1,158 +0,0 @@
-# count_mgf_peptides.py
-# -*- coding: utf-8 -*-
-
-import re
-import sys
-from pathlib import Path
-
-import pandas as pd
-
-
-SEQ_PATTERNS = [
-    re.compile(r"^SEQ\s*=\s*(.+)$", re.IGNORECASE),
-    re.compile(r"^PEPTIDE\s*=\s*(.+)$", re.IGNORECASE),
-    re.compile(r"\bSEQ\s*=\s*([^;\s]+)", re.IGNORECASE),           # inside TITLE/COMMENT
-    re.compile(r"\bSEQUENCE\s*=\s*([^;\s]+)", re.IGNORECASE),      # inside TITLE/COMMENT
-    re.compile(r"\bPep(?:tide)?\s*=\s*([^;\s]+)", re.IGNORECASE),  # Pep= / Peptide=
-]
-
-def normalize_raw(seq: str) -> str:
-    s = seq.strip().strip('"').strip("'")
-    # 截断在第一个空白处（有些 TITLE 里会把很多字段拼一起）
-    s = s.split()[0]
-    return s
-
-def strip_modifications(seq: str) -> str:
-    """
-    将修饰等非字母字符去掉，仅保留 A-Z 作为“纯肽段序列”口径。
-    例如: "M(ox)PEP[+16]TIDE" -> "MPEPTIDE"
-    """
-    s = normalize_raw(seq).upper()
-    s = re.sub(r"[^A-Z]", "", s)
-    return s
-
-def extract_peptide_from_line(line: str):
-    line = line.strip()
-    for pat in SEQ_PATTERNS[:2]:
-        m = pat.match(line)
-        if m:
-            return m.group(1).strip()
-    # 其他模式一般在 TITLE/COMMENT 这种行里
-    for pat in SEQ_PATTERNS[2:]:
-        m = pat.search(line)
-        if m:
-            return m.group(1).strip()
-    return None
-
-def parse_mgf_file(mgf_path: Path):
-    """
-    返回:
-      peptides_raw: set[str]      (原始提取到的序列/字段值)
-      peptides_stripped: set[str] (去修饰后仅A-Z)
-      spectra_cnt: int            (BEGIN IONS ... END IONS 块数)
-    """
-    peptides_raw = set()
-    peptides_stripped = set()
-    spectra_cnt = 0
-
-    in_block = False
-    current_seq = None
-
-    with mgf_path.open("r", encoding="utf-8", errors="ignore") as f:
-        for line in f:
-            s = line.strip()
-            if not s:
-                continue
-
-            up = s.upper()
-            if up.startswith("BEGIN IONS"):
-                in_block = True
-                current_seq = None
-                continue
-
-            if up.startswith("END IONS"):
-                if in_block:
-                    spectra_cnt += 1
-                    if current_seq:
-                        raw = normalize_raw(current_seq)
-                        stripped = strip_modifications(current_seq)
-                        if raw:
-                            peptides_raw.add(raw)
-                        if stripped:
-                            peptides_stripped.add(stripped)
-                in_block = False
-                current_seq = None
-                continue
-
-            if in_block:
-                seq_candidate = extract_peptide_from_line(s)
-                if seq_candidate and (current_seq is None):
-                    current_seq = seq_candidate
-
-    return peptides_raw, peptides_stripped, spectra_cnt
-
-def main():
-    # 默认：脚本同级目录下的 Data/
-    base_dir = Path(sys.argv[1]).expanduser().resolve() if len(sys.argv) > 1 else (Path(__file__).resolve().parent)
-    if not base_dir.exists():
-        print(f"[ERROR] Data directory not found: {base_dir}")
-        print("用法: python count_mgf_peptides.py /path/to/Data")
-        sys.exit(1)
-
-    mgf_files = sorted(base_dir.rglob("*.mgf"))
-    if not mgf_files:
-        print(f"[WARN] No .mgf files found under: {base_dir}")
-        sys.exit(0)
-
-    rows = []
-    global_raw = set()
-    global_stripped = set()
-
-    for p in mgf_files:
-        peptides_raw, peptides_stripped, spectra_cnt = parse_mgf_file(p)
-        global_raw |= peptides_raw
-        global_stripped |= peptides_stripped
-
-        rel = p.relative_to(base_dir)
-        organism = rel.parts[0] if len(rel.parts) >= 2 else ""
-        rows.append({
-            "organism_folder": organism,
-            "file_name": p.name,
-            "relative_path": str(rel),
-            "spectra_blocks": spectra_cnt,
-            "unique_peptides_stripped(A-Z)": len(peptides_stripped),
-            "unique_peptides_raw": len(peptides_raw),
-        })
-
-    df = pd.DataFrame(rows).sort_values(["organism_folder", "file_name"]).reset_index(drop=True)
-
-    # 汇总行
-    summary = pd.DataFrame([{
-        "organism_folder": "TOTAL",
-        "file_name": "",
-        "relative_path": "",
-        "spectra_blocks": int(df["spectra_blocks"].sum()),
-        "unique_peptides_stripped(A-Z)": len(global_stripped),
-        "unique_peptides_raw": len(global_raw),
-    }])
-
-    out_xlsx = "/Users/guanmumu/Desktop/Data/mgf_unique_peptides_summary.xlsx"
-    with pd.ExcelWriter(out_xlsx, engine="openpyxl") as writer:
-        df.to_excel(writer, index=False, sheet_name="per_file")
-        summary.to_excel(writer, index=False, sheet_name="summary")
-
-    # 可选：把全局unique peptide列表也落盘，方便你核对
-    (Path.cwd() / "global_unique_peptides_stripped.txt").write_text(
-        "\n".join(sorted(global_stripped)) + "\n", encoding="utf-8"
-    )
-    (Path.cwd() / "global_unique_peptides_raw.txt").write_text(
-        "\n".join(sorted(global_raw)) + "\n", encoding="utf-8"
-    )
-
-    print(f"[OK] Found {len(mgf_files)} MGF files under: {base_dir}")
-    print(f"[OK] Excel written to: {out_xlsx}")
-    print(f"[OK] Global unique peptides (stripped) = {len(global_stripped)}")
-    print(f"[OK] Global unique peptides (raw)      = {len(global_raw)}")
-
-if __name__ == "__main__":
-    main()