def get_variant_type(variant_source): """Try to find out what type of variants that exists in a variant source Args: variant_source (str): Path to variant source source_mode (str): 'vcf' or 'gemini' Returns: variant_type (str): 'sv' or 'snv' """ file_type = get_file_type(variant_source) variant_type = 'sv' if file_type == 'vcf': variants = VCF(variant_source) elif file_type == 'gemini': variants = GeminiQuery(variant_source) gemini_query = "SELECT * from variants" variants.run(gemini_query) # Check 1000 first variants, if anyone is a snv we set the variant_type # to 'snv' for i, variant in enumerate(variants): if file_type == 'vcf': if variant.is_snp: variant_type = 'snv' elif file_type == 'gemini': if variant['type'] == 'snp': variant_type = 'snv' if i > 1000: break return variant_type
def get_variant_type(variant_source): """Try to find out what type of variants that exists in a variant source Args: variant_source (str): Path to variant source source_mode (str): 'vcf' or 'gemini' Returns: variant_type (str): 'sv' or 'snv' """ file_type = get_file_type(variant_source) variant_type = 'sv' if file_type == 'vcf': variants = VCF(variant_source) elif file_type == 'gemini': variants = GeminiQuery(variant_source) gemini_query = "SELECT * from variants" variants.run(gemini_query) # Check 1000 first variants, if anyone is a snv we set the variant_type # to 'snv' for i,variant in enumerate(variants): if file_type == 'vcf': if variant.is_snp: variant_type = 'snv' elif file_type == 'gemini': if variant['type'] == 'snp': variant_type = 'snv' if i > 1000: break return variant_type