From dd9c8df418040093f2116de6592fc6add0c6a2ce Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 1 Jan 2021 12:09:10 +0000
Subject: genbank: cleaning up

---
 workflows/pull-data/genbank/README.md | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

(limited to 'workflows/pull-data/genbank/README.md')

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
-- 
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