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| author | AndreaGuarracino | 2020-08-23 11:28:02 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-08-23 11:28:02 +0200 |
| commit | 3b9423891c4e90499a40c1be029ef40160efb557 (patch) | |
| tree | fd3bcb6d5113161a20d71d89db18e277a2f11e8d /scripts/download_genbank_data | |
| 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/download_genbank_data')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 6 |
1 files changed, 4 insertions, 2 deletions
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 3c59f8c..f314a1d 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -316,10 +316,12 @@ 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', 'combined nasopharyngeal and 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', '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 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']: + 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', 'Nasopharyngeal/Throat']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] + elif GBQualifier_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 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']: |