Implement BWMatching solved by 277

March 18, 2014, 8:26 p.m. by Rosalind Team

We are now ready to describe BWMATCHING, an algorithm that counts the total number of matches of Pattern in Text, where the only information that we are given is FirstColumn and LastColumn = BWT(Text) in addition to the Last-to-First mapping (from “Generate the Last-to-First Mapping of a String”). The pointers top and bottom are updated by the green lines in the following pseudocode.

    BWMATCHING(FirstColumn, LastColumn, Pattern, LastToFirst)
        top ← 0
        bottom ← |LastColumn| − 1
        while top ≤ bottom
            if Pattern is nonempty
                symbol ← last letter in Pattern
                remove last letter from Pattern
                if positions from top to bottom in LastColumn contain an occurrence of symbol
                    topIndex ← first position of symbol among positions from top to bottom in LastColumn
                    bottomIndex ← last position of symbol among positions from top to bottom in LastColumn
                    top ← LastToFirst(topIndex)
                    bottom ← LastToFirst(bottomIndex)
                else
                    return 0
            else
                return bottom − top + 1

Implement BWMatching

Given: A string BWT(Text), followed by a collection of strings Patterns.

Return: A list of integers, where the i-th integer corresponds to the number of substring matches of the i-th member of Patterns in Text.

Sample Dataset

TCCTCTATGAGATCCTATTCTATGAAACCTTCA$GACCAAAATTCTCCGGC
CCT CAC GAG CAG ATC

Sample Output

2 1 1 0 1

Extra Datasets

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