miscellaneous simple bioinformatics utilities and lookup tables

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  • License: Apache Software License (Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR U...)
  • Author: biocommons contributors
  • Tags biocommons, bioinformatics, genomics, HGVS, variation
  • Requires: Python >=3.10
  • Provides-Extra: dev, docs, test
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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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Avatar for biocommons from gravatar.com biocommons Avatar for jsstevenson from gravatar.com jsstevenson Avatar for korikuzma from gravatar.com korikuzma Avatar for reece from gravatar.com reece

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  • License: Apache Software License (Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR U...)
  • Author: biocommons contributors
  • Tags biocommons, bioinformatics, genomics, HGVS, variation
  • Requires: Python >=3.10
  • Provides-Extra: dev, docs, test
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