From acdd66f36e1596f8337195f22fdd7dd8a85c2b70 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 1 Jan 2021 09:53:15 +0000
Subject: genbank-fetch-ids simple call

---
 workflows/pull-data/genbank/README.md              | 2 +-
 workflows/pull-data/genbank/genbank-fetch-ids      | 6 ++++--
 workflows/pull-data/genbank/update-from-genbank.py | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index 0204dd0..22dd920 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -6,7 +6,7 @@ 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
+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
diff --git a/workflows/pull-data/genbank/genbank-fetch-ids b/workflows/pull-data/genbank/genbank-fetch-ids
index 00f693f..24fe4c7 100755
--- a/workflows/pull-data/genbank/genbank-fetch-ids
+++ b/workflows/pull-data/genbank/genbank-fetch-ids
@@ -1,3 +1,5 @@
-#!/usr/bin/env ruby
-#
+#!/bin/sh
 #
+# genbank-fetch-ids > genbank_ids.tx
+
+curl 'https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id'
diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py
index 07bb15d..132f553 100755
--- a/workflows/pull-data/genbank/update-from-genbank.py
+++ b/workflows/pull-data/genbank/update-from-genbank.py
@@ -3,7 +3,7 @@
 # - bulk download genbank data and matadata, preparing the FASTA and
 #   the YAML files
 #
-# See .guix-run python3 from_genbank_to_fasta_and_yaml.py
+# See .guix-run
 
 import argparse
 parser = argparse.ArgumentParser()
-- 
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