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fa66973 | 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 | """调试：反向链路 —— 短 RNA（nuccore）→ 文献（pubmed）→ 摘要。
正向链路（pubmed→nuccore）实测拿到的都是 2–4 kb 的完整 mRNA，
全部超过 RNA-FM 的 1024 nt 上限，被过滤光了。
所以改用反向：**先找短 RNA 序列**，再反向找它们的文献。
"""
from __future__ import annotations
import sys
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
sys.path.insert(0, str(ROOT / "src"))
from rnaqwen.data.sources import Entrez, parse_fasta, parse_pubmed_xml # noqa: E402
QUERIES = {
"refseq_ncrna_short": 'biomol_rna[prop] AND srcdb_refseq[prop] AND 60:1000[slen] AND '
'("non-coding RNA"[Title] OR "lncRNA"[Title] OR "miRNA"[Title] '
'OR "snoRNA"[Title] OR "riboswitch"[Title] OR "ribozyme"[Title])',
"mirna_precursor": '"miRNA"[Title] AND 60:300[slen] AND biomol_rna[prop]',
"riboswitch": 'riboswitch[Title] AND 60:600[slen] AND biomol_rna[prop]',
"trna": '"tRNA"[Title] AND 60:200[slen] AND biomol_rna[prop]',
}
def main() -> int:
ez = Entrez()
for name, q in QUERIES.items():
ids = ez.esearch("nuccore", q, retmax=5)
print(f"\n=== {name} === term={q[:90]}...")
print(f" 前 5 个 nuccore id: {ids}")
if not ids:
continue
fasta = parse_fasta(ez.efetch("nuccore", ids, retmode="text", rettype="fasta"))
for acc, defn, seq in fasta:
print(f" {acc:16s} len={len(seq):5d} {defn[:80]}")
links = ez.elink("nuccore", "pubmed", ids)
n_links = sum(len(v) for v in links.values())
print(f" -> pubmed 链接数: {n_links} ({ {k: v[:3] for k, v in list(links.items())[:3]} })")
pmids = sorted({p for v in links.values() for p in v})[:3]
if pmids:
lit = parse_pubmed_xml(ez.efetch("pubmed", pmids, retmode="xml"))
for pmid, meta in list(lit.items())[:2]:
print(f" PMID {pmid}: abstract={len(meta['abstract'])} 字符 | {meta['title'][:70]}")
return 0
if __name__ == "__main__":
raise SystemExit(main())
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