From e33ce088225b9975a84a6724ab8e3a9f82964ec6 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 31 Dec 2020 10:25:26 +0000
Subject: genbank: pseudo workflow

---
 workflows/pull-data/genbank/README.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 workflows/pull-data/genbank/README.md

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

diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
new file mode 100644
index 0000000..ee67e70
--- /dev/null
+++ b/workflows/pull-data/genbank/README.md
@@ -0,0 +1,13 @@
+Pipeline:
+
+```sh
+# --- 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 --dir ~/tmp/pubseq > genbank_ids.txt
+# --- loop through IDs (pseudo code)
+for id in genbank_ids.txt:
+  transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq
+```
-- 
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