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OrthoFinder v2.5.5

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@davidemms davidemms released this 15 May 17:21
· 53 commits to master since this release
2.5.5
c85ab1d

New in this release

  • Reduce number of open files when writing orthologs to approximately one per species instead of one per species-pair, this should resolve issues related to ulimit.
  • Added option --fewer-files: Requests that OrthoFinder only write one orthologs file per species. This file will list all orthologs in all other species (the default is one file of orthologs for each species pair, listing only the orthologs between those two species).
    -- Added script scripts_of/split_ortholog_files.py to recreate one file of orthologs per species-pair from a OrthoFinder results directory produced with the --fewer-files option.
  • Dependency checks: Print debug info & preserve test files if dependency checks fail for tools that OrthoFinder calls.

Fixes:

  • 'U' file opening mode deprecated, removed
  • Use fork for multiprocessing on linux, resolves #663
  • Report top-level exceptions, resolves #673
  • Fix tools/create_files_for_hogs.py input arguments, resolves #647
  • Warn specifically if no self-hits, resolves #611
  • Fix HOGs when species removed, resolves #602
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