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| author | Pjotr Prins | 2021-01-04 09:40:54 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-04 09:40:54 +0000 |
| commit | 3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a (patch) | |
| tree | 6151f218cef5d4412118844ebce65d732f4b17b7 /workflows/pull-data | |
| parent | 1c4e055b8a9dc53b7fdbdf12d4b0a7e877fbc2ef (diff) | |
| download | bh20-seq-resource-3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a.tar.gz bh20-seq-resource-3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a.tar.lz bh20-seq-resource-3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a.zip | |
mapping sample_species using regex
Diffstat (limited to 'workflows/pull-data')
| -rw-r--r-- | workflows/pull-data/genbank/ref.py | 19 |
1 files changed, 0 insertions, 19 deletions
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py index 4d4df48..d2a377e 100644 --- a/workflows/pull-data/genbank/ref.py +++ b/workflows/pull-data/genbank/ref.py @@ -21,22 +21,3 @@ elif GBQualifier_name_text == 'collected_by': elif GBQualifier_name_text == 'isolation_source': if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']: GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' - -# Little cleaning -GBQualifier_value_text = GBQualifier_value_text.strip("/'") - -if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]] -else: - if GBQualifier_value_text.lower() in ['np/op', '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']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['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', 'Nasopharyngeal/Throat']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']: - sample['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] - else: - missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) |