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authorPeter Amstutz2020-04-30 12:28:08 -0400
committerGitHub2020-04-30 12:28:08 -0400
commitead1cfc4eebb1c150fc345983834556a23d14bac (patch)
treef2ec888cbf1cb1ebb0ad13d843aa09263463b040 /scripts
parent3b69ffa7d7f3b24a393bbf11b9de79a9eb96eac6 (diff)
parent6165495618b9c2ad3ad7b8bd95ed807d022ebf1c (diff)
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Merge pull request #47 from AndreaGuarracino/patch-15
fixed UO_0000036 for year
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py2
1 files changed, 1 insertions, 1 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 900f087..6f046ea 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -200,7 +200,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
if 'age' in GBQualifier_value_text:
info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
- info_for_yaml_dict['host']['host_age_unit'] = 'year'
+ info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
elif GBQualifier_name_text == 'collected_by':
if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text