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# 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
python3 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 (validation mode)
python3 ../../workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --species ncbi_host_species.csv --specimen specimen.csv --validate
```
# TODO
- [ ] Add id for GenBank accession - i.e. how can we tell a record is from GenBank
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