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| author | Andrea Guarracino | 2020-04-19 22:35:45 +0200 |
|---|---|---|
| committer | GitHub | 2020-04-19 22:35:45 +0200 |
| commit | 0427b3cdd1cd09d3c969ea23f56e2ca3d9c81ace (patch) | |
| tree | 531e6d3adf0677a504af6f01b5ebe48d2e197766 /scripts | |
| parent | cfb0c23c5206ea2d81794a4212d824a32a0a406b (diff) | |
| download | bh20-seq-resource-0427b3cdd1cd09d3c969ea23f56e2ca3d9c81ace.tar.gz bh20-seq-resource-0427b3cdd1cd09d3c969ea23f56e2ca3d9c81ace.tar.lz bh20-seq-resource-0427b3cdd1cd09d3c969ea23f56e2ca3d9c81ace.zip | |
added 'np/op' control for specimen_source
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/from_genbank_to_fasta_and_yaml.py | 2 |
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 33615fa..0c410d7 100644 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -186,7 +186,7 @@ if not os.path.exists(dir_fasta_and_yaml_today): 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 in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab']: + if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']: info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab'] info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab'] else: |