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12/count.py

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+# 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()

count.py

@@ -0,0 +1,158 @@
+# 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()