diff --git a/eva_cttv_pipeline/clinvar_xml_io/clinvar_xml_io/clinvar_xml_io.py b/eva_cttv_pipeline/clinvar_xml_io/clinvar_xml_io/clinvar_xml_io.py index 8dadbf13..908c0621 100644 --- a/eva_cttv_pipeline/clinvar_xml_io/clinvar_xml_io/clinvar_xml_io.py +++ b/eva_cttv_pipeline/clinvar_xml_io/clinvar_xml_io/clinvar_xml_io.py @@ -176,11 +176,11 @@ def clinical_significance_raw(self): @property def clinical_significance_list(self): - """The normalised list of all clinical significance values. The original value is (1) split into multiple values - by 3 delimiters: ('/', ', ', '; '), (2) converted into lowercase and (3) sorted lexicographically. Example: - 'Benign/Likely benign, risk_factor' → ['benign', 'likely benign', 'risk factor']. See /data-exploration/ - clinvar-variant-types/README.md for further explanation.""" - return sorted(re.split('/|, |; ', self.clinical_significance_raw.lower().replace('_', ' '))) + """The normalised deduplicated list of all clinical significance values. The original value is (1) split into + multiple values by 3 delimiters: ('/', ', ', '; '), (2) converted into lowercase and (3) sorted + lexicographically. Example: 'Benign/Likely benign, risk_factor' → ['benign', 'likely benign', 'risk factor']. + See /data-exploration/clinvar-variant-types/README.md for further explanation.""" + return sorted(list(set(re.split('/|, |; ', self.clinical_significance_raw.lower().replace('_', ' '))))) @property def allele_origins(self): diff --git a/setup.py b/setup.py index 0eccf99e..df6825bb 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ def get_requires(): setup(name='eva_cttv_pipeline', - version='2.7.2', + version='2.7.3', packages=find_packages(), install_requires=get_requires(), #! TBD: list as a dependency subpackage 'clinvar_xml_utils.clinvar_xml_utils.clinvar_xml_utils'