# GenBank

This directory contains the tools to pull and transform
GenBank data.

# Workflows

## Prepare new GenBank data for upload

The following workflow sends GenBank data into PubSeq

```sh
# --- get list of IDs already in PubSeq
../../tools/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/JSON and FASTA
python3 transform-genbank-xml2yamlfa.py --out ~/tmp/pubseq file(s)
# --- Normalize data
../../tools/normalize-yamlfa.py --in ~/tmp/pubseq/state.json file(s)
```

# TODO

- [ ] Add id for GenBank accession - i.e. how can we tell a record is from GenBank