From d35363996ce49da6c638ce768027f3a97881c2fa Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 6 Jun 2020 17:29:01 +0200
Subject: fixed collection_location when it is not present in the dictionary
 terms

---
 scripts/from_genbank_to_fasta_and_yaml.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'scripts')

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 9c8e9b9..befd64d 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -320,11 +320,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                         GBQualifier_value_text = 'China: Hong Kong'
 
                     if GBQualifier_value_text in term_to_uri_dict:
-                        GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
+                        info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text]
                     else:
                         missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text]))
-
-                    info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
                 elif GBQualifier_name_text == 'note':
                     if 'additional_collection_information' in info_for_yaml_dict['sample']:
                         info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text
-- 
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