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-rw-r--r--workflows/pull-data/genbank/README.md4
-rwxr-xr-xworkflows/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