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authorAndrea Guarracino2020-06-22 22:41:04 +0200
committerGitHub2020-06-22 22:41:04 +0200
commit21ac66de2f92b7a433c6677d7526ee8d9639d999 (patch)
treea44ed1fc5b84dc277201fefd0780cca917be8e6a /scripts
parent76883d02e6073f990ea980dad1f8cf21121255ff (diff)
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little fix for specimen_source
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py10
1 files changed, 6 insertions, 4 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 87e99d4..6216340 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -305,12 +305,14 @@ 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']:
+ 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']:
info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']]
- elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and 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']:
info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']]
- elif GBQualifier_value_text in ['nasopharyngeal aspirate/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']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['oropharyngeal swab']]
else:
missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text]))
elif GBQualifier_name_text == 'collection_date':