Release Version 0.18.0 · vanheeringen-lab/gimmemotifs

[0.18.0] - 2023-01-11

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.

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.

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