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Diffstat (limited to 'workflows/pull-data/genbank/README.md')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 19 |
1 files changed, 15 insertions, 4 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index b5bac84..d7cc15f 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -1,14 +1,25 @@ -# pipeline +# 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 -./sparql-fetch-ids > pubseq_ids.txt +../../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 and FASTA -python3 transform-genbank-xml2yamlfa --out ~/tmp/pubseq file(s) +# --- 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 |