bx.pwm package

Submodules

• bx.pwm.bed_score_aligned_pwm module
  • isnan()
  • main()
• bx.pwm.bed_score_aligned_string module
  • isnan()
  • main()
• bx.pwm.maf_select_motifs module
  • format_tabular()
  • isnan()
  • mafwrite()
  • main()
• bx.pwm.position_weight_matrix module
  • Align
  • AlignScoreMatrix
  • PositionWeightMatrix
    • PositionWeightMatrix.complementMap
    • PositionWeightMatrix.corrected_probability_score()
    • PositionWeightMatrix.correlation()
    • PositionWeightMatrix.information_base_content()
    • PositionWeightMatrix.information_content_calculation()
    • PositionWeightMatrix.max_correlation()
    • PositionWeightMatrix.parse_weight()
    • PositionWeightMatrix.pseudocount()
    • PositionWeightMatrix.pwm_score()
    • PositionWeightMatrix.scaled()
    • PositionWeightMatrix.score_align()
    • PositionWeightMatrix.score_quantum_seq()
    • PositionWeightMatrix.score_reverse_seq()
    • PositionWeightMatrix.score_seq()
    • PositionWeightMatrix.simple_probability()
    • PositionWeightMatrix.slide_correlation()
    • PositionWeightMatrix.symbols
    • PositionWeightMatrix.to_count_matrix()
    • PositionWeightMatrix.to_matrix()
  • Reader
    • Reader.close()
    • Reader.read_as_basic()
    • Reader.read_as_transfac()
    • Reader.where()
  • consensus_symbol()
  • isnan()
  • match_consensus()
  • reverse_complement()
  • rsquared()
  • score_align_gaps()
  • score_align_motif()
  • sum_of_squares()
• bx.pwm.pwm_score_maf module
  • MafBlockScorer()
  • MafMotifScorer()
  • MafMotifSelect()
  • MafScorer()
  • isnan()
  • main()
• bx.pwm.pwm_score_motifs module
  • isnan()
  • main()
• bx.pwm.pwm_score_positions module
  • isnan()
  • main()
• bx.pwm.pwm_tests module
  • PWMTestCase
    • PWMTestCase.testReader()

Module contents

Data structures and tools for working with Position Weight Matrices (PWMs).

TODO: Some of the packages in this directory are actually command line programs that provide no library functions and should be moved to the scripts directory.