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miscellaneous simple bioinformatics utilities and lookup tables

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bioutils provides some common utilities and lookup tables for bioinformatics.

  • bioutils.accessions – parse accessions, infer namespaces
  • bioutils.assemblies – Human assembly information (from NCBI/GRCh)
  • bioutils.cytobands – map cytobands to coordinates (from UCSC cytoband tables)
  • bioutils.digests – implementations of various digests
  • bioutils.normalize – allele normalization (left shuffle, right shuffle, expanded, vcf)

To use an E-Utilities API key run add it to an environment variable called ncbi_api_key and it will be used in the E-Utilities request.

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