malva.complexity module

malva.complexity.overlapping_windows(sequence, L)

Returns overlapping windows of size L from sequence sequence :type sequence: :param sequence: the nucleotide or protein sequence to scan over :type L: :param L: the length of the windows to yield

malva.complexity.compute_rep_vector(sequence, N)

Computes the repetition vector (as seen in Wooton, 1993) from a given sequence of a biopolymer with N possible residues.

Parameters:

• sequence – the nucleotide or protein sequence to generate a repetition vector for.

• N – the total number of possible residues in the biopolymer sequence belongs to.

malva.complexity.complexity(sequence, N)

Computes the Shannon Entropy of a given sequence of a biopolymer with N possible residues. See (Wooton, 1993) for more.

Parameters:

• sequence – the nucleotide or protein sequence whose Shannon Entropy is to calculated.

• N – the total number of possible residues in the biopolymer sequence belongs to.

malva.complexity.mask_low_complexity(seq_rec, maskchar='N', N=20, L=12)

Masks low-complexity nucleic/amino acid sequences with a given mask character.

Parameters:

• seq_rec – a string

• maskchar – Character to mask low-complexity residues with.

• N – Number of residues to expect in the sequence. (20 for AA, 4 for DNA)

• L – Length of sliding window that reads the sequence.