rosalindchapter2

README

Rosalind Chapter 2

This folder contains the chapter2 module, which provides functions for each of the problems from Chapter 2 of Rosalind.info's Bionformatics Textbook track.

How to run

• Each problem has its own function (example: BA2a(...))

• Each problem expects an input file (example input files in for_real directory, or provide the input file downloaded from Rosalind.info)

• Pass the input file name to the function, like this: BA2a("rosalind_ba2a.txt")

Quick Start

To use the functions in this package, start by installing it:

go get github.com/charlesreid1/go-rosalind/chapter2

Once you have installed the chapter2 package, you can import it, then call the function for whichever Rosalind.info problem you want to solve from Chapter 2:

package main

import (
    rch1 "github.com/charlesreid1/go-rosalind/chapter2"
)

func main() {
    rch1.BA2a("rosalind_ba2a.txt")
}

Examples

See chapter2_test.go for examples.

Tests

To run tests of all Chapter 2 problems, run go test from this directory:

go test -v

or, from the parent directory, the root of the go-rosalind repository:

go test -v ./chapter2/...

Note that this solves every problem in Chapter 2 and prints the solutions (so there is a lot of spew). It does not check the solutions (for that, see the tests in the rosalind library.)

Documentation

Index

• func BA2a(filename string)
• func BA2aDescription()
• func BA2b(filename string)
• func BA2bDescription()
• func BA2c(filename string)
• func BA2cDescription()
• func BA2d(filename string)
• func BA2dDescription()
• func BA2e(filename string)
• func BA2eDescription()
• func BA2f(filename string)
• func BA2fDescription()
• func BA2g(filename string)
• func BA2gDescription()

Functions

func BA2a

func BA2a(filename string)

Run the problem

func BA2aDescription

func BA2aDescription()

Print problem description for Rosalind.info Problem BA2a: Implement Motif Enumeration

func BA2b

func BA2b(filename string)

Run the problem

func BA2bDescription

func BA2bDescription()

Print problem description for Rosalind.info Problem BA2b: Find a Median String

func BA2c

func BA2c(filename string)

Run the problem

func BA2cDescription

func BA2cDescription()

Print problem description for Rosalind.info Problem BA2c: Find a Profile-most Probable k-mer in a String

func BA2d

func BA2d(filename string)

Run the problem

func BA2dDescription

func BA2dDescription()

Print problem description for Rosalind.info Problem BA2d: Implement GreedyMotifSearch

func BA2e

func BA2e(filename string)

Run the problem

func BA2eDescription

func BA2eDescription()

Print problem description for Rosalind.info Problem BA2e: Implement GreedyMotifSearch with Pseudocounts

func BA2f

func BA2f(filename string)

Run the problem

func BA2fDescription

func BA2fDescription()

Print problem description for Rosalind.info Problem BA2f: Implement RandomizedMotifSearch with Pseudocounts

func BA2g

func BA2g(filename string)

Run the problem

func BA2gDescription

func BA2gDescription()

Print problem description for Rosalind.info Problem BA2g: Implement GibbsSampler