aboutsummaryrefslogtreecommitdiff
path: root/scripts
diff options
context:
space:
mode:
authorAndreaGuarracino2020-06-06 17:29:01 +0200
committerAndreaGuarracino2020-06-06 17:29:01 +0200
commitd35363996ce49da6c638ce768027f3a97881c2fa (patch)
tree2d47c96d7cfd4d730d1f1fff10216b3742219896 /scripts
parent9f31ac441e69d4e07bf93235cfa0459a077fb00c (diff)
downloadbh20-seq-resource-d35363996ce49da6c638ce768027f3a97881c2fa.tar.gz
bh20-seq-resource-d35363996ce49da6c638ce768027f3a97881c2fa.tar.lz
bh20-seq-resource-d35363996ce49da6c638ce768027f3a97881c2fa.zip
fixed collection_location when it is not present in the dictionary terms
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py4
1 files changed, 1 insertions, 3 deletions
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