check_tcga_match.py

import argparse
import os
import re
from collections import defaultdict

def is_dir(p):
    try:
        return os.path.isdir(p)
    except Exception:
        return False

def is_file(p):
    try:
        return os.path.isfile(p)
    except Exception:
        return False

TCGA_ID_RE = re.compile(r"(TCGA-[A-Z0-9]{2}-[A-Z0-9]+)")

def extract_case_id(name):
    m = TCGA_ID_RE.search(name)
    return m.group(1) if m else None

def collect_from_dir(path):
    items = []
    for n in os.listdir(path):
        if n.startswith('.'):
            continue
        items.append(n)
    cases = set()
    case_to_items = defaultdict(list)
    for n in items:
        cid = extract_case_id(n)
        if cid:
            cases.add(cid)
            case_to_items[cid].append(n)
    return items, cases, case_to_items

def collect_from_file(path):
    items = []
    with open(path, 'r', encoding='utf-8', errors='ignore') as f:
        for line in f:
            line = line.strip()
            if not line:
                continue
            items.append(line)
    cases = set()
    case_to_items = defaultdict(list)
    for n in items:
        cid = extract_case_id(n)
        if cid:
            cases.add(cid)
            case_to_items[cid].append(n)
    return items, cases, case_to_items

def collect(path):
    if is_dir(path):
        return collect_from_dir(path)
    if is_file(path):
        return collect_from_file(path)
    raise FileNotFoundError(path)

def main():
    ap = argparse.ArgumentParser()
    ap.add_argument('--feature_source', type=str, default='/mnt/datadisk0/TCGA_pt/MESO_UNI')
    ap.add_argument('--label_source', type=str, default='/mnt/datadisk0/datasets/TCGA-MESO')
    ap.add_argument('--limit', type=int, default=50)
    args = ap.parse_args()

    feat_items, feat_cases, feat_map = collect(args.feature_source)
    lab_items, lab_cases, lab_map = collect(args.label_source)

    common = sorted(feat_cases & lab_cases)
    miss_labels = sorted(feat_cases - lab_cases)
    miss_features = sorted(lab_cases - feat_cases)

    print('Feature source:', args.feature_source)
    print('Total feature items:', len(feat_items))
    print('Feature cases:', len(feat_cases))
    print('Label source:', args.label_source)
    print('Total label items:', len(lab_items))
    print('Label cases:', len(lab_cases))
    print('Matched cases:', len(common))

    if miss_labels:
        print('Cases present in features but missing labels:', len(miss_labels))
        for cid in miss_labels[:args.limit]:
            print(cid, 'feature_count=', len(feat_map.get(cid, [])))
        if len(miss_labels) > args.limit:
            print('... and', len(miss_labels) - args.limit, 'more')
    else:
        print('No cases missing labels')

    if miss_features:
        print('Cases present in labels but missing features:', len(miss_features))
        for cid in miss_features[:args.limit]:
            print(cid)
        if len(miss_features) > args.limit:
            print('... and', len(miss_features) - args.limit, 'more')
    else:
        print('No cases missing features')

    top_counts = sorted(((cid, len(feat_map[cid])) for cid in common), key=lambda x: (-x[1], x[0]))
    if top_counts:
        print('Top matched cases by feature count:')
        for cid, c in top_counts[:min(args.limit, 20)]:
            print(cid, 'feature_count=', c)

if __name__ == '__main__':
    main()