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Published September 1, 2020 | Version 0.9.0
Software Open

vanheeringen-lab/genomepy: Version 0.9.0

Authors/Creators

  • 1. Radboud University
  • 2. @bhi-kimlab
  • 3. @github

Description

[0.9.0] - 2020-09-01 Added
  • check to see if providers are online + error message if not
  • automatic provider selection for genomepy install
    • optional provider flag for genomepy install (-p/--provider)
    • if no provider is passed to genomepy install, the first provider with the genome is used (order: Ensembl > UCSC > NCBI).
  • genomepy clean removes local caches. Will be reloaded when required.
Changed
  • Ensembl genomes always download over ftp (http was too unstable)
  • Ensembl release versions obtained via REST API (http was too unstable)
  • genomepy search and genomepy providers only check online providers
  • Online function now have a timeout and a retry system
  • API changes to download_genome and download_annotation for consistency
Fixed
  • Ensembl status check uses lighter url (more stable)
  • search and install now consistently use safe search terms (no spaces)
  • search now uses UTF-8, no longer crashing for \u2019 (some quotation mark).
  • search case insensitivity fixed for assembly names.
  • Bucketcache now stores less data, increasing responsiveness.

Files

vanheeringen-lab/genomepy-0.9.0.zip

Files (496.2 kB)

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md5:6c3b5ff094a852217b27060ce7e13f37
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Additional details

Related works

Is supplement to
https://github.com/vanheeringen-lab/genomepy/tree/0.9.0 (URL)