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| author | Pjotr Prins | 2021-01-01 12:09:10 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-01 12:09:10 +0000 |
| commit | dd9c8df418040093f2116de6592fc6add0c6a2ce (patch) | |
| tree | 723c6976953159b0a17ea2c2c3b78480832b64be /workflows/pull-data/genbank/README.md | |
| parent | acdd66f36e1596f8337195f22fdd7dd8a85c2b70 (diff) | |
| download | bh20-seq-resource-dd9c8df418040093f2116de6592fc6add0c6a2ce.tar.gz bh20-seq-resource-dd9c8df418040093f2116de6592fc6add0c6a2ce.tar.lz bh20-seq-resource-dd9c8df418040093f2116de6592fc6add0c6a2ce.zip | |
genbank: cleaning up
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 |