gumpy

Genetics with numpy. Utilises numpy arrays internally for improved speed when parsing genomes and assigning promoters.

Provides features including

• Parsing genbank files to produce Genome (and Gene) objects;
• Handle assignment of promoter regions to genes within a genome;
• Parsing VCF files to produce VCFFile (and VCFRecord) objects;
• Applying a VCF file to a reference genome to produce a new genome;
• Finding in-depth differences between two genomes such as indels;
• Finding in-depth differences caused by a VCF such as SNPs, het and null calls;
• Finding in-depth differences between two genes such as SNPs, indels and mutations in GARC;
• Handle intricacies of genomes such as reverse complement genes and -1 PRF.