Merge branch 'master' into yamlfa2ttl

1 files changed, 13 insertions, 12 deletions

diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py
index dca5563..95f5a93 100755
--- a/workflows/pull-data/genbank/update-from-genbank.py
+++ b/workflows/pull-data/genbank/update-from-genbank.py
@@ -14,22 +14,21 @@ import sys
 from utils import chunks
 
 from Bio import Entrez
-Entrez.email = 'another_email@gmail.com' # FIXME
 
-BATCH=100
+Entrez.email = 'another_email@gmail.com'  # FIXME
+
+BATCH = 100
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--max', type=int, help='Max queries', required=False)
 parser.add_argument('--ids', type=str, help='File with ids to fetch, 1 id per line', required=True)
 parser.add_argument('--out', type=str, help='Directory to write to', required=True)
+parser.add_argument('--max', type=int, help='Max queries', required=False)
 
 args = parser.parse_args()
 
 ids = set()
 with open(args.ids) as f:
-    content = f.readlines()
-    for line in content:
-        ids.add(line.strip())
+    ids.update([line.strip() for line in f])
 
 dir = args.out
 if not os.path.exists(dir):
@@ -37,12 +36,14 @@ if not os.path.exists(dir):
 
 request_num = BATCH
 if args.max:
-  request_num = min(BATCH,args.max)
+    request_num = min(BATCH, args.max)
+
+for num_chunk, ids_chunk in enumerate(chunks(list(ids), request_num)):
+    xmlfn = os.path.join(dir, f"metadata_{num_chunk}.xml.gz")
+    print(f"Fetching {xmlfn} ({num_chunk * request_num})", file=sys.stderr)
 
-for i, idsx in enumerate(chunks(list(ids), request_num)):
-    xmlfn = os.path.join(dir, f"metadata_{i}.xml.gz")
-    print(f"Fetching {xmlfn} ({i*request_num})",file=sys.stderr)
     with gzip.open(xmlfn, 'w') as f:
-        f.write((Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read()).encode())
-    if args.max and i*request_num >= args.max:
+        f.write(Entrez.efetch(db='nuccore', id=ids_chunk, retmode='xml').read().encode())
+
+    if args.max and num_chunk * request_num >= args.max:
         break