diff options
Diffstat (limited to 'workflows/pull-data')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 4 | ||||
| -rwxr-xr-x | workflows/pull-data/genbank/genbank-fetch-ids.py (renamed from workflows/pull-data/genbank/update-from-genbank.py) | 0 |
2 files changed, 3 insertions, 1 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index c235be7..f442b5d 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -3,8 +3,10 @@ ```sh # --- get list of IDs already in PubSeq sparql-fetch-ids > pubseq_ids.txt +# --- get list of missing genbank IDs +genbank-fetch-ids --skip pubseq_ids.txt > genbank_ids.txt # --- fetch XML -update-from-genbank.py --skip pubseq_ids.txt --outdir ~/tmp/genbank +update-from-genbank.py --ids genbank_ids.txt --outdir ~/tmp/genbank # --- Transform to YAML and FASTA transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq ``` diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/genbank-fetch-ids.py index e62a611..e62a611 100755 --- a/workflows/pull-data/genbank/update-from-genbank.py +++ b/workflows/pull-data/genbank/genbank-fetch-ids.py |