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# ---- BELOW IS JUST FOR REFERENCE ----
if field_in_yaml == 'sequencing_coverage':
# A regular expression would be better!
try:
technology[field_in_yaml] = [
float(tech_info_to_parse.replace('(average)', '').replace("reads/nt", '').
replace('(average for 6 sequences)', '').replace(',', '.').strip(' xX>'))
]
except ValueError:
print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
pass
elif GBQualifier_name_text == 'collected_by':
if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
sample['collecting_institution'] = GBQualifier_value_text
else:
sample['collector_name'] = GBQualifier_value_text
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]))
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