Module vcf_rider::pwm [−] [src]

Module representing Positional Weight Matrixes and that is able to compute their score on a given sequence.

Re-exports

use std::io;

use std::io::prelude::*;

use std::io::BufReader;

use std::fs::File;

use std::iter::Iterator;

use rider::CanScoreSequence;

Matrix	Struct used to represent PWM likelihoods/nucleotide frequencies. ncols is used to be able to represent 4 and 5 nucleotides PWMs (to manage N in sequences). No consistency checks are performed for get/set operations for efficiency.
PWM	Struct representing a whole Positional Weight Matrix.
PWMReader	Struct used to read PWM. It will be implement an Iterator of `PWM` structs. The String buffer is used to get characters from the `BufReader` one by one and load the `freq` for the loaded `PWM` structs. The expected format is the same used by matrix_rider in C, therefore a tab delimited file with these columns: pwm_name, pos, count_a, count_c, count_g, count_t pos is ignored, count_x should be positive integer different from 0.