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| author | Pjotr Prins | 2021-01-01 10:59:56 -0600 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-01 10:59:56 -0600 |
| commit | a029c2329e748874bee88317e44d3f47547f71d8 (patch) | |
| tree | 2ef6d412ff5ba3aae61c74898e7b2738ba4e6bc3 /workflows/pull-data/genbank/README.md | |
| parent | 3f059ebde6fe6888e62f4fc232d05fb3a322b011 (diff) | |
| download | bh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.tar.gz bh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.tar.lz bh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.zip | |
genbank: minor fixes
Diffstat (limited to 'workflows/pull-data/genbank/README.md')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index 479ddc9..5597234 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -2,11 +2,11 @@ ```sh # --- get list of IDs already in PubSeq -sparql-fetch-ids > pubseq_ids.txt +./sparql-fetch-ids > pubseq_ids.txt # --- get list of missing genbank IDs -genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt +./genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt # --- fetch XML -update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank +python3 update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank # --- Transform to YAML and FASTA transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq ``` |