Python annotate_effects Examples

Example #1

File: variation.py Project: mcicdata/bcbb

def variation_effects(vrn_file, genome_file, genome_build, config):
    """Calculate effects of variations, associating them with transcripts.
    """
    snpeff_vcf, snpeff_txt = snpeff_effects(vrn_file, genome_build, config)
    annotated_vcf = annotate_effects(vrn_file, snpeff_vcf, genome_file, config) \
                    if snpeff_vcf else None
    return annotated_vcf, snpeff_txt

Example #2

File: variation.py Project: rwness/bcbb

def variation_effects(vrn_file, genome_file, genome_build, config):
    """Calculate effects of variations, associating them with transcripts.
    """
    snpeff_vcf, snpeff_txt = snpeff_effects(vrn_file, genome_build, config)
    annotated_vcf = annotate_effects(vrn_file, snpeff_vcf, genome_file, config) \
                    if snpeff_vcf else None
    return annotated_vcf, snpeff_txt