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| author | Andrea Guarracino | 2020-06-22 22:41:04 +0200 |
|---|---|---|
| committer | GitHub | 2020-06-22 22:41:04 +0200 |
| commit | 21ac66de2f92b7a433c6677d7526ee8d9639d999 (patch) | |
| tree | a44ed1fc5b84dc277201fefd0780cca917be8e6a | |
| parent | 76883d02e6073f990ea980dad1f8cf21121255ff (diff) | |
| download | bh20-seq-resource-21ac66de2f92b7a433c6677d7526ee8d9639d999.tar.gz bh20-seq-resource-21ac66de2f92b7a433c6677d7526ee8d9639d999.tar.lz bh20-seq-resource-21ac66de2f92b7a433c6677d7526ee8d9639d999.zip | |
little fix for specimen_source
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 87e99d4..6216340 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -305,12 +305,14 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]] else: - if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab']: + if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']] - elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab']: + elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] - elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] + elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']] + elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['oropharyngeal swab']] else: missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': |