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| author | AndreaGuarracino | 2020-06-06 17:29:01 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-06-06 17:29:01 +0200 |
| commit | d35363996ce49da6c638ce768027f3a97881c2fa (patch) | |
| tree | 2d47c96d7cfd4d730d1f1fff10216b3742219896 | |
| parent | 9f31ac441e69d4e07bf93235cfa0459a077fb00c (diff) | |
| download | bh20-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
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 4 |
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 |