File size: 3,412 Bytes
a8a75c9 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | 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()
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