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hyphenrf's solution

to Hamming in the MIPS Assembly Track

Published at Jul 30 2020 · 0 comments
Instructions
Test suite
Solution

Calculate the Hamming difference between two DNA strands.

A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.

The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.

By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.

This is called the 'Hamming distance'.

It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

The Hamming distance between these two DNA strands is 7.

Implementation notes

The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.

Source

The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/

Submitting Incomplete Solutions

It's possible to submit an incomplete solution so you can see how others have completed the exercise.

runner.mips

#
# Test hamming_distance with some examples
#
# s0 - num of tests left to run
# s1 - address of input word 1
# s2 - address of input word 2
# s3 - address of expected output word
# s4 - char byte
# s5 - output word
#
# hamming_distance must:
# - be named hamming_distance and declared as global
# - read input address of first string from a0
# - read input address of second string from a1
# - follow the convention of using the t0-9 registers for temporary storage
# - (if it uses s0-7 then it is responsible for pushing existing values to the stack then popping them back off before returning)
# - write integer result to v0

.data

# number of test cases
n: .word 13
# input values (null terminated) & expected output values (word sized ints)
xs: .asciiz "A", "GGACTGA", "A", "AG", "AT", "GGACG", "ACCAGGG", "AGA", "AGG", "TAG", "GATACA", "GGACGGATTCTG", ""
ys: .asciiz "A", "GGACTGA", "G", "CT", "CT", "GGTCG", "ACTATGG", "AGG", "AGA", "GAT", "GCATAA", "AGGACGGATTCT", ""
outs: .word   0,         0,   1,    2,    1,       1,         2,     1,     1,     2,        4,              9,  0

failmsg: .asciiz "failed for test inputs: "
comma: .asciiz ", "
expectedmsg: .asciiz ". expected "
tobemsg: .asciiz " to be "
okmsg: .asciiz "all tests passed"


.text

runner:
        lw      $s0, n
        la      $s1, xs
        la      $s2, ys
        la      $s3, outs

run_test:
        move    $a0, $s1                # move address of input arg 1 to a0
        move    $a1, $s2                # move address of input arg 2 to a0
        jal     hamming_distance        # call subroutine under test
        move    $v1, $v0                # move return value in v0 to v1 because we need v0 for syscall

        lw      $s5, 0($s3)             # read expected output from memory
        bne     $v1, $s5, exit_fail     # if expected doesn't match actual, jump to fail

scan:
        addi    $s1, $s1, 1             # move input address one byte forward
        addi    $s2, $s2, 1
        lb      $s4, 0($s1)             # load byte
        beq     $s4, $zero, done_scan   # if char null, break loop
        j       scan                    # loop

done_scan:
        addi    $s1, $s1, 1             # move input address one byte past null
        addi    $s2, $s2, 1

        addi    $s3, $s3, 4             # move to next word in output
        sub     $s0, $s0, 1             # decrement num of tests left to run
        bgt     $s0, $zero, run_test    # if more than zero tests to run, jump to run_test

exit_ok:
        la      $a0, okmsg              # put address of okmsg into a0
        li      $v0, 4                  # 4 is print string
        syscall

        li      $v0, 10                 # 10 is exit with zero status (clean exit)
        syscall

exit_fail:
        la      $a0, failmsg            # put address of failmsg into a0
        li      $v0, 4                  # 4 is print string
        syscall

        move    $a0, $s1                # print input that failed on
        li      $v0, 4
        syscall

        la      $a0, expectedmsg
        li      $v0, 4
        syscall

        move    $a0, $v1                # print actual that failed on
        li      $v0, 1                  # 1 is print integer
        syscall

        la      $a0, tobemsg
        li      $v0, 4
        syscall

        move    $a0, $s5                # print expected value that failed on
        li      $v0, 1                  # 1 is print integer
        syscall

        li      $a0, 1                  # set error code to 1
        li      $v0, 17                 # 17 is exit with error
        syscall

# # Include your implementation here if you wish to run this from the MARS GUI.
# .include "impl.mips"
.globl hamming_distance

.text
hamming_distance:
	li    $v0, 0
LOOP:
	lb    $t0, ($a0)
	lb    $t1, ($a1)

	beqz  $t0, STOP 	#test strings are always of the same length
	addi  $a0, $a0, 1
	addi  $a1, $a1, 1

	beq   $t0, $t1, LOOP	#continue if they're equal, else: 
	addi  $v0, $v0, 1	#..incr v0
	j     LOOP		#..then continue
STOP:
	jr    $ra

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