How to resolve the algorithm Bioinformatics/base count step by step in the Forth programming language
Published on 12 May 2024 09:40 PM
How to resolve the algorithm Bioinformatics/base count step by step in the Forth programming language
Table of Contents
Problem Statement
Given this string representing ordered DNA bases:
Let's start with the solution:
Step by Step solution about How to resolve the algorithm Bioinformatics/base count step by step in the Forth programming language
Source code in the forth programming language
( Gforth 0.7.3 )
: dnacode s" CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTGTCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT" ;
variable #A \ Gforth initialises variables to 0
variable #C
variable #G
variable #T
variable #ch
50 constant pplength
: basecount ( adr u -- )
." Sequence:"
swap dup rot + swap ?do \ count while pretty-printing
#ch @ pplength mod 0= if cr #ch @ 10 .r 2 spaces then
i c@ dup emit
dup 'A = if drop #A @ 1+ #A ! else
dup 'C = if drop #C @ 1+ #C ! else
dup 'G = if drop #G @ 1+ #G ! else
dup 'T = if drop #T @ 1+ #T ! else drop then then then then
#ch @ 1+ #ch !
loop
cr cr ." Base counts:"
cr 4 spaces 'A emit ': emit #A @ 5 .r
cr 4 spaces 'C emit ': emit #C @ 5 .r
cr 4 spaces 'G emit ': emit #G @ 5 .r
cr 4 spaces 'T emit ': emit #T @ 5 .r
cr ." ----------"
cr ." Sum:" #ch @ 5 .r
cr ." ==========" cr cr
;
( demo run: )
dnacode basecount
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