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| author | AndreaGuarracino | 2020-09-28 11:57:51 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-09-28 11:57:51 +0200 |
| commit | c72dab2788d010153d5406f2d5ecbe3824571931 (patch) | |
| tree | 668ced54cfa0c27274f81cccc71397679bb63e26 /scripts/download_genbank_data | |
| parent | bc2e51bc8418876cc826482ece10874b2a61fa03 (diff) | |
| download | bh20-seq-resource-c72dab2788d010153d5406f2d5ecbe3824571931.tar.gz bh20-seq-resource-c72dab2788d010153d5406f2d5ecbe3824571931.tar.lz bh20-seq-resource-c72dab2788d010153d5406f2d5ecbe3824571931.zip | |
new countries; updated genbank/sra scripts to manage more specimen sources
Diffstat (limited to 'scripts/download_genbank_data')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 2 |
1 files changed, 1 insertions, 1 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 9b8fedc..364090e 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 @@ -305,7 +305,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']: info_for_yaml_dict['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 swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: + 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']: info_for_yaml_dict['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']: info_for_yaml_dict['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']] |