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Version 0.18.0

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@siebrenf siebrenf released this 11 Jan 12:51
0.18.0
7451274

[0.18.0] - 2023-01-11

Added

  • gimme scan and gimme maelstrom now accept a random seed for (most) operations
    • for (optimal) deterministic behaviour, delete the cache and then run the command with a seed
  • Scanner now accepts a np.random.RandomState and progress on init.
    • progress=None (the default) should print progress bars to the command line only, not to file.
  • Scanner.set_genome now accepts the optional argument genomes_dir
  • gimmemotifs.maelstrom.Moap.create now accepts a np.random.RandomState.
  • gimmemotifs.maelstrom.run_maelstrom now accepts a np.random.RandomState.

Changed

  • gimme diff (diff_plot() to be exact) will now print to stdout, like all other functions
  • now using the logger instead of print/sys.stderr.write in many more places
  • string formatting now (mostly) done with f-strings
  • refactored Fasta class
  • split scanner.py into 3 submodules:
    • scanner/__init__.py with the exported functions
    • scanner/base.py with the Scanner class
    • scanner/utils.py with the rest
  • gimmemotifs/maelstrom.py renamed to gimmemotifs/maelstrom/_init__.py
    • rank.py and moap.py are now submodules of maelstrom.

Fixed

  • gimme maelstrom works with or without xgboost (but will give a warning without xgboost)
  • fixed warning "in validate_matrix(): Row sums in df are not close to 1. Reormalizing rows..."
  • fixed multiprocess.Pool Warnings
  • fixed a pandas copywarning (in gc_bin_bedfile() to be exact)
  • fixed warnings when leaving files open
  • fixed deprecation warning in maelstrom (and in tests)
  • fixed futurewarning in report.py
  • silence warnings from external tools in motif prediction (pp_predict_motifs() to be exact)
  • updated last references from Motif.pwm_scan and Motif.pwm_scan_all to Motif.scan and Motif.scan_all respectively
  • typo in gimme motifs output ("%matches background" to "% matches background")
  • Scanner now uses a cheaper method to determine a genome's identity
    • (filesize + name instead of the md5sum of the whole genome's contents)
  • gimme motifs gives an informative error when fraction is not within 0-1.
  • gimme threshold works again

Removed

  • removed old python2 code (scanning with MOODS & import shenanigans)
Assets 3