diff options
| author | AndreaGuarracino | 2020-08-23 11:28:02 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-08-23 11:28:02 +0200 |
| commit | 3b9423891c4e90499a40c1be029ef40160efb557 (patch) | |
| tree | fd3bcb6d5113161a20d71d89db18e277a2f11e8d /scripts/create_sra_metadata | |
| parent | 634e266777c7a2e67a4e998845061e250615675a (diff) | |
| download | bh20-seq-resource-3b9423891c4e90499a40c1be029ef40160efb557.tar.gz bh20-seq-resource-3b9423891c4e90499a40c1be029ef40160efb557.tar.lz bh20-seq-resource-3b9423891c4e90499a40c1be029ef40160efb557.zip | |
genbank/sra scripts update to be more generic with the specimen sources
Diffstat (limited to 'scripts/create_sra_metadata')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 6 |
1 files changed, 4 insertions, 2 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index d02fde8..0e1215e 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -128,10 +128,12 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]] else: - if VALUE_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab']: + if VALUE_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']] - elif 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']: + elif 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', 'Nasopharyngeal/Throat']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] + elif VALUE_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] elif 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 VALUE_text.lower() in ['nasal-swab and oro-pharyngeal swab']: |