From 764bd98fcfdde9657c520fb9bfcfb775ea9f05c9 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Fri, 13 Nov 2020 13:39:23 +0100
Subject: fix in the ids to consider

---
 scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 083122f..5a8a336 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -120,8 +120,12 @@ if not os.path.exists(dir_metadata):
     with open(path_ncbi_virus_accession) as f:
         tmp_list = [line.strip('\n') for line in f]
 
-    new_ids = len(set(tmp_list).difference(id_set))
-    id_set.update(tmp_list)
+    new_ids_set = set(tmp_list)
+    if len(accession_to_consider_set) > 0:
+        new_ids_set = new_ids_set.intersection(accession_to_consider_set)
+
+    new_ids = len(new_ids_set.difference(id_set))
+    id_set.update(new_ids_set)
 
     print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
 
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