diff options
Diffstat (limited to 'workflows/pull-data/genbank/README.md')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 9 |
1 files changed, 3 insertions, 6 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index 22dd920..c235be7 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -4,12 +4,9 @@ # --- get list of IDs already in PubSeq sparql-fetch-ids > pubseq_ids.txt # --- fetch XML -update-from-genbank --skip pubseq_ids.txt --max 100 --outdir ~/tmp/genbank -# --- get new IDs -genbank-fetch-ids > genbank_ids.txt -# --- loop through IDs (pseudo code) -for id in genbank_ids.txt: - transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq +update-from-genbank.py --skip pubseq_ids.txt --outdir ~/tmp/genbank +# --- Transform to YAML and FASTA +transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq ``` # TODO |