bioin.motif.count_motif

bioin.motif.count_motif(motifs)

Count the number of nucleotides (4 types: ACGT) column wise from a motifs matrix.

Parameters:motifs (list) – list of DNA strings, stack to constitute of the motifs matrix in genome. Returns:Dictionary, the count of each nucleotides in each column of the motifs matrix.

Examples

Takes a list of strings motifs as input and returns the count matrix of motifs (as a dictionary of lists.)

>>> motifs = ['AACGTA', 'CCCGTT', 'CACCTT', 'GGATTA', 'TTCCGG']
>>> counts_dict = count_motif(motifs)
>>> counts_dict
    {'A': [1, 2, 1, 0, 0, 2], 'C': [2, 1, 4, 2, 0, 0], 'G': [1, 1, 0, 2, 1, 1], 'T': [1, 1, 0, 1, 4, 2]}