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Version 1.5.0: SemiBin2 beta

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@luispedro luispedro released this 17 Jan 11:11
· 109 commits to main since this release
v1.5.0
fc0d22c

Big change is the addition of a SemiBin2 script, which is still experimental, but should be a slightly nicer interface.

User-visible improvements since v1.4.0

  • Added a new option for ORF finding, called fast-naive which is an internal very fast implementation.
  • Added the possibility of bypassing ORF finding altogether by providing prodigal outputs directly (or any other gene prediction in the right format)
  • Command line argument checking is more exhaustive instead of exiting at first error
  • Added --quiet flag to reduce the amount of output printed
  • Better --help (group required arguments separately)
  • Add --output-compression option to compress outputs
  • Add --tag-output option which allows for control of the output filenames (and also makes the anvi'o compatible — see discussion at #123.
  • Add contig->bin mapping table (#123)
  • SemiBin.main.main1 and SemiBin.main.main2 can now be called as a function with command line arguments (main1 corresponds to SemiBin1 and main2 corresponds to SemiBin2)
import SemiBin.main    
    
...    
    
SemiBin.main.main2(['single_easy_bin', '--input-fasta', ...])
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