blob: 559723467e8d5beee2dd1bbbd4e8ce692d4c50c5 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
|
# pipeline
```sh
# --- get list of IDs already in PubSeq
./sparql-fetch-ids > pubseq_ids.txt
# --- get list of missing genbank IDs
./genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
# --- fetch XML
python3 update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank
# --- Transform to YAML and FASTA
transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq
```
# TODO
- [ ] Add id for GenBank accession - i.e. how can we tell a record is from GenBank
|
