From 3f059ebde6fe6888e62f4fc232d05fb3a322b011 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 1 Jan 2021 16:24:37 +0000
Subject: gzip output

---
 workflows/pull-data/genbank/update-from-genbank.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'workflows')

diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py
index 6d6d90c..d92f87a 100755
--- a/workflows/pull-data/genbank/update-from-genbank.py
+++ b/workflows/pull-data/genbank/update-from-genbank.py
@@ -8,6 +8,7 @@
 # See also directory .guix-run and README.md
 
 import argparse
+import gzip
 import os
 import sys
 from utils import chunks
@@ -35,9 +36,9 @@ if not os.path.exists(dir):
 
 request_num = min(BATCH,args.max)
 for i, idsx in enumerate(chunks(list(ids), request_num)):
-    xmlfn = os.path.join(dir, f"metadata_{i}.xml")
+    xmlfn = os.path.join(dir, f"metadata_{i}.xml.gz")
     print(f"Fetching {xmlfn} ({i*request_num})",file=sys.stderr)
-    with open(xmlfn, 'w') as f:
-        f.write(Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read())
+    with gzip.open(xmlfn, 'w') as f:
+        f.write((Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read()).encode())
     if i*request_num >= args.max:
         break
-- 
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