diff options
Diffstat (limited to 'scripts/create_sra_metadata/create_sra_metadata.py')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 18 |
1 files changed, 14 insertions, 4 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 352a30e..0e1215e 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -23,14 +23,19 @@ term_to_uri_dict = {} for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]: print('Read {}'.format(path_dict_xxx_csv)) - with open(path_dict_xxx_csv, 'r') as f: + with open(path_dict_xxx_csv) as f: for line in f: if len(line.split(',')) > 2: term, uri = line.strip('\n').split('",') - term = term.strip('"') else: term, uri = line.strip('\n').split(',') + term = term.strip('"') + + if term in term_to_uri_dict: + print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term)) + continue + term_to_uri_dict[term] = uri def is_integer(string_to_check): @@ -123,10 +128,12 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]] else: - if 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 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 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 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 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 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 VALUE_text.lower() in ['nasal-swab and oro-pharyngeal swab']: @@ -178,6 +185,9 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): else: info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text) elif TAG_text == 'geo_loc_name': + if ': ' in VALUE_text: + VALUE_text = VALUE_text.replace(': ', ':') + if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text] elif VALUE_text.lower() not in ['na', 'not applicable']: |