Version 0.17.0

Changelog

[0.17.0] - 2021-12-22

Added

• Added --genomes_dir argument to gimme motif2factors.
• Added --version flag.
• Function sample() for fast sequence sampling from a Motif() instance.
• Added JASPAR 2022 motif databases.
• Updated Homer motif database.
• Operators:
  • + - take the combination of two motifs (average), based on pfm, which means that motifs with higher counts will be weighed more heavily.
  • & - take the combination of two motifs (average), based on the ppm, which means that both motifs will be weighed equally.
  • << - "shift" motif left (adding a non-informative position to the right side)
  • >> - "shift" motif right (adding a non-informative position to the left side)
  • ~ - reverse complement
  • * - multiply the pfm by a value
• Progress bar for scanning.
• list_installed_libraries() to list available motif libraries.

Changed

• Motif() class completely restructured:
  • Split into multiple files with coherent function.
  • Uses numpy.array internally.
  • All functions that mention pwm renamed to ppm (position-probability matrix), as the definition of a PWM is usually a log-odds matrix, not a probability matrix.
    • to_pwm() is deprecated, use to_ppm() instead.
  • Changed functions pwm_min_score() and pwm_max_score() to properties max_score and min_score.
  • All internal data is correctly updated when Motif() is changed, for instance by trimming (#218).

Fixed

• gimme motif2factors can now unzip genome fastas.
• gimme motif2factors will sanitize genome names.
• Fixed bugs related to partial rerun of gimme motif2factors.
• Fixed unhandled OSError during installation on Mac.
• Fixed bug related to RFE() (#226).
• Positional probability matrix now sum to 1 over all positions (#209).
• Fixed issue with pandas >= 1.3.
• Fixed issue with non_reducing_slice import from pandas.
• Fix threshold calculation if more than 20,000 sequences are supplied.
• Fix issue with config file getting corrupted.
• Fix FPR threshold calculation.