Add solution to BA2F (#17 )

* add a maxint and minint utility function * add problems ba2f and ba2g * remove ba2g for now * adding BA2f to chapter 2 problems * add BA2f solution (failing) * remove expensive test * fix random motif generator script (random number problems) * fix how we aggregate over multiple random motif searches * call random motif search multiple times * update BA2F so eet wurk * make tests a lil easier * add ba2f input file, whoops * add ba2g - gibbs sampler * update BA2g solution with bug fixes * add ba2g to chapter 2 tests. add ba2g input file.
add a maxint and minint utility function (#16 )
119 changed files with 50262 additions and 1831 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,3 +1,9 @@
 golibby
 queens
 chapter01/chapter01
 # golang:
 # Binaries for programs and plugins
 *.exe
 *.exe~
--- a/.travis.yml
+++ b/.travis.yml
@ -0,0 +1,14 @@
 # https://docs.travis-ci.com/user/languages/go/
 language: go
 go: 
 - 1.10.x
 - 1.11.x
 - tip
 install: true
 script:
 - go test -v ./rosalind/...
 - go test -v ./chapter1/...
 - go test -v ./chapter2/...
 - go test -v ./chapter3/...
--- a/19
+++ b/19
@ -0,0 +1,19 @@
 Copyright 2019 Charles Reid
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in
 the Software without restriction, including without limitation the rights to
 use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
 of the Software, and to permit persons to whom the Software is furnished to do
 so, subject to the following conditions:
 The above copyright notice and this permission notice shall be included in all
 copies or substantial portions of the Software.
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
--- a/Readme.md
+++ b/Readme.md
@ -1,41 +1,126 @@
-# Go-Rosalind
+# go-rosalind
-Solving problems from Rosalind.info using Go
+`rosalind` is a Go (golang) package for solving bioinformatics problems.
-## Organization
+[![travis](https://img.shields.io/travis/charlesreid1/go-rosalind.svg)](https://travis-ci.org/charlesreid1/go-rosalind.svg)
 [![golang](https://img.shields.io/badge/language-golang-00ADD8.svg)](https://golang.org)
 [![license](https://img.shields.io/github/license/charlesreid1/go-rosalind.svg)](https://github.com/charlesreid1/go-rosalind/blob/master/LICENSE)
 [![godoc](https://godoc.org/github.com/charlesreid1/go-rosalind?status.svg)](http://godoc.org/github.com/charlesreid1/go-rosalind)
 ## Summary
-Each chapter has its own directory.
+This repo contains a Go (golang) library, `rosalind`, that implements
 functionality for solving bioinformatics problems. This is mainly
 useful for problems on Rosalind.info but is for general use as well.
-Within the chapter directory, each problem has 
+Rosalind problems are grouped by chapter. Each problem has its own 
-its own driver program, which prints info about
+function and is implemented in a library called `chapter1`, `chapter2`,
-the problem, loads the input file from Rosalind,
+etc.
 and prints the solution. Each problem also has
 its own test suite using the examples provided
 on Rosalind.info.
-For example, the function that loads the 
+For example, Chapter 1 question A is implemented in package
-input file for problem BA1A is in `ba1a.go`
+`chapter1` as the function `BA1a( <input-file-name> )`. 
-and the code to test the functionality
+This (specific) functionality wraps the (general purpose)
-of the solution to BA1A is in `ba1a_test.go`.
+`rosalind` library.
 ## Quick Start
-To run all the tests in a chapter directory:
+### Rosalind
 The `rosalind` library can be installed using `go get`:
 ```
 go get https://github.com/charlesreid1/go-rosalind/rosalind
 ```
 The library can now be imported and its functions called directly.
 Here is a brief example:
 ```
 package main
 import (
    "fmt"
    "github.com/charlesreid1/go-rosalind/rosalind"
 )
 func main() {
    input := "AAAATGCGCTAGTAAAAGTCACTGAAAA"
    k := 4
    result, _ := rosalind.MostFrequentKmers(input, k)
    fmt.Println(result)
 }
 ```
-go test -v
+
 ### Problem Sets
 Each set of problems is grouped into its own package. These
 packages import the `rosalind` package, so it should be
 available.
 You can install the Chapter 1 problem set, for example, like so:
 ```
 go get https://github.com/charlesreid1/go-rosalind/chapter1
 ```
 This can now be imported and used in any Go program. 
 Try creating a `main.go` file in a temporary directory,
 and run it with `go run main.go`:
 ```
 package main
-To run only a particular problem:
+import (
    rch1 "github.com/charlesreid1/go-rosalind/chapter1"
 )
-1. Edit `main.go` to call the right method
+func main() {
-   for the right problem with the right input
+    filename := "rosalind_ba1a.txt"
-   file name.
+    rch1.BA1a(filename)
 }
 ```
-2. Run `main.go` using `go run`, and point Go
+Assuming an input file `rosalind_ba1a.txt` is available,
-   to all the relevant Go files:
+you should see a problem description and the output of
 the problem, which can be copied and pasted into
 Rosalind.info:
 ```
-go run main.go utils.go rosalind.go <name-of-BA-file>
+$ go run main.go
 -----------------------------------------
 Rosalind: Problem BA1a:
 Most Frequest k-mers
 Given an input string and a length k,
 report the k-mer or k-mers that occur
 most frequently.
 URL: http://rosalind.info/problems/ba1a/
 Computed result from input file: for_real/rosalind_ba1a.txt
 39
 ```
 ## Command Line Interface
 TBA
 ## Organization
 The repo contains the following directories:
 * `rosalind/` - code and functions for the Rosalind library
 * `chapter1/` - solutions to chapter 1 questions (utilizes `rosalind` library)
 * `chapter2/` - solutions to chapter 2 questions
 * `chapter3/` - solutions to chapter 3 questions
 * `stronghold/` - solutions to questions from the stronghold section of Rosalind.info
 See the Readme file in each respective directory for more info.
--- a/chapter01/Readme.md
+++ b/chapter01/Readme.md
@ -1,73 +0,0 @@
 # Chapter 1
 In this chapter we perform basic operations with 
 strings and data structures.
 ## How to run
 * Each problem has its own function
 * To run the code for a particular problem,
  call the function for that problem in `main.go`
 * Edit `main.go` to call the right function,
  and pass in the name of the input file you 
  want to use: for example, `BA1A("input.txt")`
 * The function you call is implemented in the
  corresponding Go file (for example, `ba1a.go`).
  It loads the inputs from the input file,
  calls the right function with the inputs,
  and prints the results.
 * The functions that load data from input files
  are tested along with the functions themselves,
  since each problem has a sample input file 
  in `data/`
 ## Directory Layout
 * Each problem has one Go file and one test
 * The `data/` directory contains input files
  for the tests (i.e., files that contain both
  inputs and corresponding outputs)
 * The `for_real/` directory contains sample 
  input files from Rosalind.info for each
  problem (i.e., files that contain only the
  inputs)
 * The `main.go` file contains the `main()` 
  driver function and is the entrypoint for
  `go run`
 * The `rosalind.go` file contains most of the
  computational functionality implemented
  for the problems.
 * The `utils.go` file contains utilties unrelated
  to bioinformatics.
 ## Compiling and Running
 To run all tests, `go test`:
 ```
 go test -v
 ```
 To run a specific problem, edit `main.go`
 to call the corresponding problem's function
 and then `go run`:
 ```
 go run main.go utils.go rosalind.go <name of ba1 file.go> 
 ```
 ## To Do
 Add a Snakefile
--- a/chapter01/ba1a.go
+++ b/chapter01/ba1a.go
@ -1,54 +0,0 @@
 package main
 import (
    "fmt"
    "log"
 )
 // Rosalind: Problem BA1A: Most Frequent k-mers
 // Describe the problem
 func BA1ADescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1A:",
        "Most Frequest k-mers",
        "",
        "Given an input string and a length k,",
        "report the k-mer or k-mers that occur",
        "most frequently.",
        "",
        "URL: http://rosalind.info/problems/ba1a/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem,
 // print the name of the input file,
 // print the output/result
 func BA1A(filename string) {
    BA1ADescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("readLines: %v",err)
    }
    // Input file contents
    var input, pattern string
    input   = lines[0]
    pattern = lines[1]
    result := PatternCount(input, pattern)
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(result)
 }
--- a/chapter01/ba1a_test.go
+++ b/chapter01/ba1a_test.go
@ -1,99 +0,0 @@
 package main
 import (
    "fmt"
    "log"
    "strconv"
    "testing"
 )
 // To run this test:
 //
 // $ go test -v -run TestPatternCount
 // Run a single test of the PatternCount function
 func TestPatternCount(t *testing.T) {
    // Call the PatternCount function
    input := "GCGCG"
    pattern := "GCG"
    result := PatternCount(input,pattern)
    gold := 2
    if result != gold {
        err := fmt.Sprintf("Error testing PatternCount(): input = %s, pattern = %s, result = %d (should be %d)",
            input, pattern, result, gold)
        t.Error(err)
    }
 }
 // Run a test matrix of the PatternCount function
 func TestMatrixPatternCount(t *testing.T) {
    // Construct a test matrix
    var tests = []struct {
 		input    string
        pattern  string
 		gold int
 	}{
 		{"GCGCG",        "GCG",      2},
 		{"GAGGGGGGGAG",  "AGG",      1},
 		{"GCACGCACGCAC", "GCAC",     3},
        {"",             "GC",       0},
        {"GCG",          "GTACTCTC", 0},
        {"ACGTACGTACGT", "CG",       3},
        {"AAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAATAATTACAGAGTACACAACATCCA",
                         "AAA",      4},
        {"AGCGTGCCGAAATATGCCGCCAGACCTGCTGCGGTGGCCTCGCCGACTTCACGGATGCCAAGTGCATAGAGGAAGCGAGCAAAGGTGGTTTCTTTCGCTTTATCCAGCGCGTTAACCACGTTCTGTGCCGACTTT",
                         "TTT",      4},
        {"GGACTTACTGACGTACG","ACT",  2},
        {"ATCCGATCCCATGCCCATG","CC", 5},
        {"CTGTTTTTGATCCATGATATGTTATCTCTCCGTCATCAGAAGAACAGTGACGGATCGCCCTCTCTCTTGGTCAGGCGACCGTTTGCCATAATGCCCATGCTTTCCAGCCAGCTCTCAAACTCCGGTGACTCGCGCAGGTTGAGT",
                         "CTC",      9},
 	}
    for _, test := range tests {
        result := PatternCount(test.input, test.pattern)
        if result != test.gold {
            err := fmt.Sprintf("Error testing PatternCount(): input = %s, pattern = %s, result = %d (should be %d)",
                        test.input, test.pattern, result, test.gold)
            t.Error(err)
        }
    }
 }
 // Load a PatternCount test (input and output)
 // from a file. Run the test with the input
 // and verify the output matches the output
 // contained in the file.
 func TestPatternCountFile(t *testing.T) {
    filename := "data/pattern_count.txt"
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("readLines: %v",err)
    }
    // lines[0]: Input
    input   := lines[1]
    pattern := lines[2]
    // lines[3]: Output
    output_str := lines[4]
    // Convert output to inteter
    output,err := strconv.Atoi(output_str)
    if err!=nil {
        t.Error(err)
    }
    // Call the function with the given inputs
    result := PatternCount(input, pattern)
    // Verify answer
    if result != output {
        err := fmt.Sprintf("Error testing PatternCount using test case from file: results do not match:\rcomputed result = %d\nexpected output = %d",result,output)
        t.Error(err)
    }
 }
--- a/chapter01/ba1b.go
+++ b/chapter01/ba1b.go
@ -1,58 +0,0 @@
 package main
 import (
    "fmt"
    "log"
    "strings"
    "strconv"
 )
 // Rosalind: Problem BA1B: Most Frequent k-mers
 // Describe the problem
 func BA1BDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1B:",
        "Most Frequest k-mers",
        "",
        "Given an input string and a length k,",
        "report the k-mer or k-mers that occur",
        "most frequently.",
        "",
        "URL: http://rosalind.info/problems/ba1b/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1B(filename string) {
    BA1BDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    input := lines[0]
    k_str := lines[1]
    k,err := strconv.Atoi(k_str)
    if err!=nil {
        log.Fatalf("Error: string to int conversion: %v",err)
    }
    mfks,_ := MostFrequentKmers(input,k)
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(strings.Join(mfks," "))
 }
--- a/chapter01/ba1b_test.go
+++ b/chapter01/ba1b_test.go
@ -1,82 +0,0 @@
 package main
 import (
    "fmt"
    "sort"
    "strconv"
    "strings"
    "log"
    "testing"
 )
 // Run a test of the MostFrequentKmers function
 func TestMostFrequentKmers(t *testing.T) {
    // Call MostFrequentKmers
    input := "AAAATGCGCTAGTAAAAGTCACTGAAAA"
    k := 4
    result,err := MostFrequentKmers(input,k)
    gold := []string{"AAAA"}
    if err!=nil {
        t.Error(err)
    }
    if !EqualStringSlices(result,gold) {
        err := fmt.Sprintf("Error testing MostFrequentKmers(): input = %s, k = %d, result = %s (should be %s)",
            input, k, result, gold)
        t.Error(err)
    }
 }
 // Run a test of the PatternCount function
 // using inputs/outputs from a file.
 func TestMostFrequentKmersFile(t *testing.T) {
    filename := "data/frequent_words.txt"
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("readLines: %v",err)
    }
    // lines[0]: Input
    dna   := lines[1]
    k_str := lines[2]
    // lines[3]: Output
    gold  := strings.Split(lines[4]," ")
    // Convert k to integer
    k,err := strconv.Atoi(k_str)
    if err!=nil {
        t.Error(err)
    }
    // Call the function with the given inputs
    result, err := MostFrequentKmers(dna,k)
    // Check if function threw error
    if err!=nil {
        t.Error(err)
    }
    // Check that there _was_ a result
    if len(result)==0 {
        err := fmt.Sprintf("Error testing MostFrequentKmers using test case from file: length of most frequent kmers found was 0: %q",
                result)
        t.Error(err)
    }
    // Sort before comparing
    sort.Strings(gold)
    sort.Strings(result)
    // These will only be unequal if something went wrong
    if !EqualStringSlices(gold,result) {
        err := fmt.Sprintf("Error testing MostFrequentKmers using test case from file: most frequent kmers mismatch.\ncomputed = %q\ngold     = %q\n",
                result,gold)
        t.Error(err)
    }
 }
--- a/chapter01/ba1c.go
+++ b/chapter01/ba1c.go
@ -1,50 +0,0 @@
 package main
 import (
    "fmt"
    "log"
 )
 // Rosalind: Problem BA1C: Find the Reverse Complement of a String
 // Describe the problem
 func BA1CDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1C:",
        "Find the Reverse Complement of a String",
        "",
        "Given a DNA input string,",
        "find the reverse complement",
        "of the DNA string.",
        "",
        "URL: http://rosalind.info/problems/ba1c/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1C(filename string) {
    BA1CDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    input := lines[0]
    result,_ := ReverseComplement(input)
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(result)
 }
--- a/chapter01/ba1c_test.go
+++ b/chapter01/ba1c_test.go
@ -1,123 +0,0 @@
 package main
 import (
    "fmt"
    "testing"
 )
 // Check that the DNA2Bitmasks utility
 // extracts the correct bitmasks from
 // a DNA input string.
 func TestDNA2Bitmasks(t *testing.T) {
    input := "AATCCGCT"
    result, func_err := DNA2Bitmasks(input)
    // Handle errors from in the DNA2Bitmasks function
    if func_err != nil {
        err := fmt.Sprintf("Error in function DNA2Bitmasks(): input = %s", input)
        t.Error(err)
    }
    // Assemble gold standard answer (bitvectors)
    tt := true
    ff := false
    gold := make(map[string][]bool)
    gold["A"] = []bool{tt,tt,ff,ff,ff,ff,ff,ff}
    gold["T"] = []bool{ff,ff,tt,ff,ff,ff,ff,tt}
    gold["C"] = []bool{ff,ff,ff,tt,tt,ff,tt,ff}
    gold["G"] = []bool{ff,ff,ff,ff,ff,tt,ff,ff}
    // Verify result from DNA2Bitmasks is same as 
    // our gold standard
    for _,cod := range "ATCG" {
        cods := string(cod)
        if !EqualBoolSlices(result[cods],gold[cods]) {
            err := fmt.Sprintf("Error testing DNA2Bitmasks(): input = %s, codon = %s, extracted = %v, gold = %v",
                        input, cods, result[cods], gold[cods])
            t.Error(err)
        }
    }
 }
 // Check that the Bitmasks2DNA utility
 // constructs the correct DNA string 
 // from bitmasks.
 func TestBitmasks2DNA(t *testing.T) {
    // Assemble input bitmasks
    tt := true
    ff := false
    input := make(map[string][]bool)
    input["A"] = []bool{tt,tt,ff,ff,ff,ff,ff,ff}
    input["T"] = []bool{ff,ff,tt,ff,ff,ff,ff,tt}
    input["C"] = []bool{ff,ff,ff,tt,tt,ff,tt,ff}
    input["G"] = []bool{ff,ff,ff,ff,ff,tt,ff,ff}
    gold := "AATCCGCT"
    result, func_err := Bitmasks2DNA(input)
    // Handle errors from in the DNA2Bitmasks function
    if func_err != nil {
        err := fmt.Sprintf("Error in function Bitmasks2DNA(): function returned error")
        t.Error(err)
    }
    // Verify result from DNA2Bitmasks is same as 
    // our gold standard
    if result != gold {
        err := fmt.Sprintf("Error testing Bitmasks2DNA(): result = %s, gold = %s", result, gold)
        t.Error(err)
    }
 }
 // Run a test of the function that computes
 // the ReverseComplement of a DNA string.
 func TestReverseComplement(t *testing.T) {
    input := "AAAACCCGGT"
    result,_ := ReverseComplement(input)
    gold := "ACCGGGTTTT"
    if result!=gold {
        err := fmt.Sprintf("Error testing ReverseComplement(): input = %s, result = %s (should be %s)",
            input, result, gold)
        t.Error(err)
    }
 }
 // Run a test of the ReverseComplement function
 // using inputs/outputs from a file.
 func TestReverseComplementFile(t *testing.T) {
    filename := "data/reverse_complement.txt"
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        t.Error(err)
    }
    // lines[0]: Input
    input := lines[1]
    // lines[2]: Output
    gold := lines[3]
    // Call the function with the given inputs
    result, err := ReverseComplement(input)
    // Check that there _was_ a result
    if len(result)==0 {
        err := fmt.Sprintf("Error testing ReverseComplement using test case from file")
        t.Error(err)
    }
    if result!=gold {
        err := fmt.Sprintf("Error testing ReverseComplement(): input = %s, result = %s (should be %s)",
            input, result, gold)
        t.Error(err)
    }
 }
--- a/chapter01/ba1d.go
+++ b/chapter01/ba1d.go
@ -1,61 +0,0 @@
 package main
 import (
    "fmt"
    "strconv"
    "strings"
    "log"
 )
 // Rosalind: Problem BA1D: Find all occurrences of pattern in string
 // Describe the problem
 func BA1DDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1D:",
        "Find all occurrences of pattern in string",
        "",
        "Given a string input (genome) and a substring (pattern),",
        "return all starting positions in the genome where the",
        "pattern occurs in the genome.",
        "",
        "URL: http://rosalind.info/problems/ba1d/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1D(filename string) {
    BA1DDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    pattern := lines[0]
    genome  := lines[1]
    // Result is a slice of ints
    locs,_ := FindOccurrences(pattern,genome)
    // Convert to a slice of strings for easier printing
    locs_str := make([]string,len(locs))
    for i,j := range locs {
        locs_str[i] = strconv.Itoa(j)
    }
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(strings.Join(locs_str," "))
 }
--- a/chapter01/ba1d_test.go
+++ b/chapter01/ba1d_test.go
@ -1,97 +0,0 @@
 package main
 import (
    "fmt"
    "log"
    "strings"
    "strconv"
    "testing"
 )
 func TestFindOccurrences(t *testing.T) {
    // Call FindOccurrences
    pattern := "ATAT"
    genome := "GATATATGCATATACTT"
    result,err := FindOccurrences(pattern,genome)
    gold := []int{1,3,9}
    if !EqualIntSlices(result,gold) || err!=nil {
        err := fmt.Sprintf("Error testing FindOccurrences(): result = %q, should be %q",
            result, gold)
        t.Error(err)
    }
 }
 func TestFindOccurrencesDebug(t *testing.T) {
    // Construct a test matrix
    var tests = []struct {
        pattern  string
 		genome   string
 		gold     []int
 	}{
        {"ACAC",    "TTTTACACTTTTTTGTGTAAAAA",
                []int{4}},
        {"AAA",     "AAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAATAATTACAGAGTACACAACATCCAT",
                []int{0,46,51,74}},
        {"TTT",     "AGCGTGCCGAAATATGCCGCCAGACCTGCTGCGGTGGCCTCGCCGACTTCACGGATGCCAAGTGCATAGAGGAAGCGAGCAAAGGTGGTTTCTTTCGCTTTATCCAGCGCGTTAACCACGTTCTGTGCCGACTTT",
                []int{88,92,98,132}},
        {"ATA",     "ATATATA",
                []int{0,2,4}},
 	}
    for _, test := range tests {
        result,err := FindOccurrences(test.pattern, test.genome)
        if err!=nil {
            t.Error(err)
        }
        if !EqualIntSlices(result,test.gold) {
            err := fmt.Sprintf("Error testing FindOccurrences(): result = %q, should be %q",
                result, test.gold)
            t.Error(err)
        }
    }
 }
 func TestFindOccurrencesFiles(t *testing.T) {
    filename := "data/pattern_matching.txt"
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // lines[0]: Input
    pattern := lines[1]
    genome  := lines[2]
    // lines[3]: Output
    gold_str := lines[4]
    gold_slice := strings.Split(gold_str," ")
    gold := make([]int,len(gold_slice))
    for i,g := range gold_slice {
        gold[i],err = strconv.Atoi(g)
        if err!=nil {
            t.Error(err)
        }
    }
    result,err := FindOccurrences(pattern,genome)
    if err!=nil {
        t.Error(err)
    }
    if !EqualIntSlices(result,gold) {
        err := fmt.Sprintf("Error testing FindOccurrences():\nresult = %v\ngold   = %v\n",
            result, gold)
        t.Error(err)
    }
 }
--- a/chapter01/ba1e.go
+++ b/chapter01/ba1e.go
@ -1,58 +0,0 @@
 package main
 import (
    "fmt"
    "log"
    "strings"
    "strconv"
 )
 // Rosalind: Problem BA1E: Find patterns forming clumps in a string
 // Describe the problem
 func BA1EDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1E:",
        "Find patterns forming clumps in a string",
        "",
        "A clump is characterized by integers L and t",
        "if there is an interval in the genome of length L",
        "in which a given pattern occurs t or more times.",
        "",
        "URL: http://rosalind.info/problems/ba1e/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1E(filename string) {
    BA1EDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    genome := lines[0]
    params_str := lines[1]
    params_slice := strings.Split(params_str," ")
    k,_ := strconv.Atoi(params_slice[0])
    L,_ := strconv.Atoi(params_slice[1])
    t,_ := strconv.Atoi(params_slice[2])
    patterns,_ := FindClumps(genome,k,L,t)
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(strings.Join(patterns," "))
 }
--- a/chapter01/ba1e_test.go
+++ b/chapter01/ba1e_test.go
@ -1,42 +0,0 @@
 package main
 import (
    "fmt"
    "testing"
 )
 func TestMatrixFindClumps(t *testing.T) {
    var tests = []struct {
        genome  string
        k       int
        L       int
        t       int
        gold    []string
    }{
        {"CGGACTCGACAGATGTGAAGAACGACAATGTGAAGACTCGACACGACAGAGTGAAGAGAAGAGGAAACATTGTAA",
                5, 50, 4,
                []string{"CGACA","GAAGA"}},
        {"AAAACGTCGAAAAA",
                2,  4, 2,
                []string{"AA"}},
        {"ACGTACGT",
                1,  5, 2,
                []string{"A","C","G","T"}},
        {"CCACGCGGTGTACGCTGCAAAAAGCCTTGCTGAATCAAATAAGGTTCCAGCACATCCTCAATGGTTTCACGTTCTTCGCCAATGGCTGCCGCCAGGTTATCCAGACCTACAGGTCCACCAAAGAACTTATCGATTACCGCCAGCAACAATTTGCGGTCCATATAATCGAAACCTTCAGCATCGACATTCAACATATCCAGCG",
                3,  25,   3,
                []string{"AAA","CAG","CAT","CCA","GCC","TTC"}},
    }
    for _, test := range tests {
        result,err := FindClumps(test.genome,
                test.k, test.L, test.t)
        if err!=nil {
            t.Error(err)
        }
        if !EqualStringSlices(result,test.gold) {
            err := fmt.Sprintf("Error testing FindClumps(): k = %d, L = %d, t = %d",test.k,test.L,test.t)
            t.Error(err)
        }
    }
 }
--- a/chapter01/ba1f.go
+++ b/chapter01/ba1f.go
@ -1,60 +0,0 @@
 package main
 import (
    "fmt"
    "strings"
    "strconv"
    "log"
 )
 // Rosalind: Problem BA1F: Find positions in a gene that minimizing skew
 // Describe the problem
 func BA1FDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1F:",
        "Find positions in a gene that minimize skew",
        "",
        "The skew of a genome is defined as the difference",
        "between the number of C codons and the number of G",
        "codons. Given a DNA string, this function should",
        "compute the cumulative skew for each position in",
        "the genome, and report the indices where the skew",
        "value is minimzed.",
        "",
        "URL: http://rosalind.info/problems/ba1f/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1F(filename string) {
    BA1FDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    genome := lines[0]
    minskew,_ := MinSkewPositions(genome)
    minskew_str := make([]string,len(minskew))
    for i,j := range minskew {
        minskew_str[i] = strconv.Itoa(j)
    }
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(strings.Join(minskew_str," "))
 }
--- a/chapter01/ba1f_test.go
+++ b/chapter01/ba1f_test.go
@ -1,53 +0,0 @@
 package main
 import (
    "fmt"
    "sort"
    "testing"
 )
 func TestMatrixMinSkewPosition(t *testing.T) {
    var tests = []struct {
        genome  string
        gold    []int
    }{
        {"CCTATCGGTGGATTAGCATGTCCCTGTACGTTTCGCCGCGAACTAGTTCACACGGCTTGATGGCAAATGGTTTTTCCGGCGACCGTAATCGTCCACCGAG",
                []int{53, 97}},
        {"TAAAGACTGCCGAGAGGCCAACACGAGTGCTAGAACGAGGGGCGTAAACGCGGGTCCGA",
                []int{11, 24}},
        {"ACCG",
                []int{3}},
        {"ACCC",
                []int{4}},
        {"CCGGGT",
                []int{2}},
        {"CCGGCCGG",
                []int{2,6}},
    }
    for _, test := range tests {
        // Do it - find the positions that minimize skew
        result,err := MinSkewPositions(test.genome)
        if err!=nil {
            t.Error(err)
        }
        // Check length of result
        if len(result)!=len(test.gold) {
            err := fmt.Sprintf("Error testing MinSkewPositions():\nfor genome: %s\nlength of result (%d) did not match length of gold standard (%d).\nFound: %v\nShould be: %v",
                    test.genome, len(result), len(test.gold),
                    result, test.gold)
            t.Error(err)
        }
        // Sort before comparing
        sort.Ints(result)
        sort.Ints(test.gold)
        if !EqualIntSlices(result,test.gold) {
            err := fmt.Sprintf("Error testing MinSkewPositions():\nfor genome: %s\nfound: %v\nshould be: %v",
                    test.genome, result, test.gold)
            t.Error(err)
        }
    }
 }
--- a/chapter01/ba1g.go
+++ b/chapter01/ba1g.go
@ -1,52 +0,0 @@
 package main
 import (
    "fmt"
    "log"
 )
 // Rosalind: Problem BA1G: Find Hamming distance between two DNA strings
 // Describe the problem
 func BA1GDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1G:",
        "Find Hamming distance between two DNA strings",
        "",
        "The Hamming distance between two strings HammingDistance(p,q)",
        "is the number of characters different between the two",
        "strands. This program computes the Hamming distance",
        "between two strings.",
        "",
        "URL: http://rosalind.info/problems/ba1g/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1G(filename string) {
    BA1GDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    p := lines[0]
    q := lines[1]
    hamm,_ := HammingDistance(p,q)
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(hamm)
 }
--- a/chapter01/ba1g_test.go
+++ b/chapter01/ba1g_test.go
@ -1,49 +0,0 @@
 package main
 import (
    "fmt"
    "testing"
 )
 func TestMatrixHammingDistance(t *testing.T) {
    var tests = []struct {
        p    string
        q    string
        dist int
    }{
        {"GGGCCGTTGGT",
         "GGACCGTTGAC",
          3 },
        {"AAAA",
         "TTTT",
          4 },
        {"ACGTACGT",
         "TACGTACG",
          8 },
        {"ACGTACGT",
         "CCCCCCCC",
          6 },
        {"ACGTACGT",
         "TGCATGCA",
          8 },
        {"GATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATAC",
         "AATAGCAGCTTCTCAACTGGTTACCTCGTATGAGTAAATTAGGTCATTATTGACTCAGGTCACTAACGTC",
          15 },
        {"AGAAACAGACCGCTATGTTCAACGATTTGTTTTATCTCGTCACCGGGATATTGCGGCCACTCATCGGTCAGTTGATTACGCAGGGCGTAAATCGCCAGAATCAGGCTG",
         "AGAAACCCACCGCTAAAAACAACGATTTGCGTAGTCAGGTCACCGGGATATTGCGGCCACTAAGGCCTTGGATGATTACGCAGAACGTATTGACCCAGAATCAGGCTC",
          28 },
    }
    for _, test := range tests {
        result,err := HammingDistance(test.p, test.q)
        if err!=nil {
            t.Error(err)
        }
        if result!=test.dist {
            err := fmt.Sprintf("Error testing HammingDistance(): computed dist = %d (should be %d)\np = %s\nq = %s\n",
                    result, test.dist,
                    test.p, test.q)
            t.Error(err)
        }
    }
 }
--- a/chapter01/ba1h.go
+++ b/chapter01/ba1h.go
@ -1,65 +0,0 @@
 package main
 import (
    "fmt"
    "strconv"
    "strings"
    "log"
 )
 // Rosalind: Problem BA1H: Find approximate occurrences of pattern in string
 // Describe the problem
 func BA1HDescription() {
    description := []string{
        "-----------------------------------------",
        "Rosalind: Problem BA1H:",
        "Find approximate occurrences of pattern in string",
        "",
        "Given a string Text and a string Pattern, and a maximum",
        "Hamming distance d, return all locations in Text where",
        "there is an approximate match with Pattern (i.e., a pattern",
        "with a Hamming distance from Pattern of d or less).",
        "",
        "URL: http://rosalind.info/problems/ba1h/",
        "",
    }
    for _, line := range description {
        fmt.Println(line)
    }
 }
 // Describe the problem, and call the function
 func BA1H(filename string) {
    BA1HDescription()
    // Read the contents of the input file
    // into a single string
    lines, err := readLines(filename)
    if err != nil {
        log.Fatalf("Error: readLines: %v",err)
    }
    // Input file contents
    pattern := lines[0]
    text := lines[1]
    d_str := lines[2]
    d,_ := strconv.Atoi(d_str)
    approx,_ := FindApproximateOccurrences(pattern,text,d)
    approx_str := make([]string,len(approx))
    for i,j := range approx {
        approx_str[i] = strconv.Itoa(j)
        if err!=nil {
            log.Fatalf("Error: conversion from int to string: %v",err)
        }
    }
    fmt.Println("")
    fmt.Printf("Computed result from input file: %s\n",filename)
    fmt.Println(strings.Join(approx_str," "))
 }
--- a/chapter01/ba1h_test.go
+++ b/chapter01/ba1h_test.go
@ -1,56 +0,0 @@
 package main
 import (
    "fmt"
    "testing"
 )
 func TestMatrixApproximateOccurrences(t *testing.T) {
    var tests = []struct {
        pattern string
        text    string
        d       int
        gold    []int
    }{
        {"ATTCTGGA",
         "CGCCCGAATCCAGAACGCATTCCCATATTTCGGGACCACTGGCCTCCACGGTACGGACGTCAATCAAATGCCTAGCGGCTTGTGGTTTCTCCTACGCTCC",
         3,
         []int{6, 7, 26, 27, 78}},
        {"AAA",
         "TTTTTTAAATTTTAAATTTTTT",
         2,
         []int{4, 5, 6, 7, 8, 11, 12, 13, 14, 15}},
        {"GAGCGCTGG",
         "GAGCGCTGGGTTAACTCGCTACTTCCCGACGAGCGCTGTGGCGCAAATTGGCGATGAAACTGCAGAGAGAACTGGTCATCCAACTGAATTCTCCCCGCTATCGCATTTTGATGCGCGCCGCGTCGATT",
         2,
         []int{0, 30, 66}},
        {"AATCCTTTCA",
         "CCAAATCCCCTCATGGCATGCATTCCCGCAGTATTTAATCCTTTCATTCTGCATATAAGTAGTGAAGGTATAGAAACCCGTTCAAGCCCGCAGCGGTAAAACCGAGAACCATGATGAATGCACGGCGATTGCGCCATAATCCAAACA",
         3,
         []int{3, 36, 74, 137}},
        {"CCGTCATCC",
         "CCGTCATCCGTCATCCTCGCCACGTTGGCATGCATTCCGTCATCCCGTCAGGCATACTTCTGCATATAAGTACAAACATCCGTCATGTCAAAGGGAGCCCGCAGCGGTAAAACCGAGAACCATGATGAATGCACGGCGATTGC",
         3,
         []int{0, 7, 36, 44, 48, 72, 79, 112}},
        {"TTT",
         "AAAAAA",
         3,
         []int{0, 1, 2, 3}},
        {"CCA",
         "CCACCT",
         0,
         []int{0}},
    }
    for _, test := range tests {
        result,err := FindApproximateOccurrences(test.pattern, test.text, test.d)
        if err!=nil {
            t.Error(err)
        }
        if !EqualIntSlices(result, test.gold) {
            err := fmt.Sprintf("Error testing FindApproximateOccurrences:\ncomputed = %v\ngold     = %v",
                    result, test.gold)
            t.Error(err)
        }
    }
 }
--- a/chapter01/main.go
+++ b/chapter01/main.go
@ -1,15 +0,0 @@
 package main
 import (
 )
 func main() {
    //BA1A("for_real/rosalind_ba1a.txt")
    //BA1B("for_real/rosalind_ba1b.txt")
    //BA1C("for_real/rosalind_ba1c.txt")
    //BA1D("for_real/rosalind_ba1d.txt")
    //BA1E("for_real/rosalind_ba1e.txt")
    //BA1F("for_real/rosalind_ba1f.txt")
    //BA1G("for_real/rosalind_ba1g.txt")
    BA1H("for_real/rosalind_ba1h.txt")
 }
--- a/chapter01/rosalind.go
+++ b/chapter01/rosalind.go
@ -1,545 +0,0 @@
 package main
 import (
    "fmt"
    "sort"
    "errors"
    s "strings"
 )
 /*
 rosalind.go:
 This file contains core functions that 
 are used to solve Rosalind problems.
 */
 ////////////////////////////////
 // BA1A
 // Count occurrences of a substring pattern 
 // in a string input
 func PatternCount(input string, pattern string) int {
    // Number of substring overlaps
    var overlap = len(input) - len(pattern) + 1
    // If overlap < 1, we are looking 
    // for a pattern longer than our input
    if overlap<1 {
        return 0
    }
    // Count of occurrences
    count:=0
    // Loop over each substring overlap
    for i:=0; i<overlap; i++ {
        // Grab a slice of the full input
        start:=i
        end:=i+len(pattern)
        var slice = input[start:end]
        if slice==pattern {
            count += 1
        }
    }
    return count
 }
 ////////////////////////////////
 // BA1B
 // Return the histogram of kmers of length k 
 // found in the given input
 func KmerHistogram(input string, k int) (map[string]int,error) {
    result := map[string]int{}
    if len(input)<1 {
        err := fmt.Sprintf("Error: input string was not DNA. Only characters ATCG are allowed, you had %s",input)
        return result, errors.New(err)
    }
    // Number of substring overlaps
    overlap := len(input) - k + 1
    // If overlap < 1, we are looking
    // for kmers longer than our input
    if overlap<1 {
        return result,nil
    }
    // Iterate over each position,
    // extract the string,
    // increment the count.
    for i:=0; i<overlap; i++ {
        // Get the kmer of interest
        substr := input[i:i+k]
        // If it doesn't exist, the value is 0
        result[substr] += 1
    }
    return result,nil
 }
 // Find the most frequent kmer(s) in the kmer histogram,
 // and return as a string array slice
 func MostFrequentKmers(input string, k int) ([]string,error) {
    max := 0
    // most frequent kmers
    mfks := []string{}
    if k<1 {
        err := fmt.Sprintf("Error: MostFrequentKmers received a kmer size that was not a natural number: k = %d",k)
        return mfks, errors.New(err)
    }
    khist,err := KmerHistogram(input,k)
    if err != nil {
        err := fmt.Sprintf("Error: MostFrequentKmers failed when calling KmerHistogram()")
        return mfks, errors.New(err)
    }
    for kmer,freq := range khist {
        if freq > max {
            // We have a new maximum, and a new set of kmers
            max = freq
            mfks = []string{kmer}
        } else if freq==max {
            // We have another maximum
            mfks = append(mfks,kmer)
        }
    }
    return mfks,nil
 }
 // Find the kmer(s) in the kmer histogram
 // exceeding a count of N, and return as
 // a string array slice
 func MoreFrequentThanNKmers(input string, k, N int) ([]string,error) {
    // more frequent than n kmers
    mftnks := []string{}
    if k<1 || N<1 {
        err := fmt.Sprintf("Error: MoreFrequentThanNKmers received a kmer or frequency size that was not a natural number: k = %d, N = %d",k,N)
        return mftnks, errors.New(err)
    }
    khist,err := KmerHistogram(input,k)
    if err != nil {
        err := fmt.Sprintf("Error: MoreFrequentThanNKmers failed when calling KmerHistogram()")
        return mftnks, errors.New(err)
    }
    for kmer,freq := range khist {
        if freq >= N {
            // Add another more frequent than n
            mftnks = append(mftnks,kmer)
        }
    }
    return mftnks,nil
 }
 ////////////////////////////////
 // BA1C
 // Reverse returns its argument string reversed 
 // rune-wise left to right.
 // https://github.com/golang/example/blob/master/stringutil/reverse.go
 func ReverseString(s string) string {
    r := []rune(s)
    for i, j := 0, len(r)-1; i < len(r)/2; i, j = i+1, j-1 {
        r[i], r[j] = r[j], r[i]
    }
    return string(r)
 }
 // Given an alleged DNA input string,
 // iterate through it character by character
 // to ensure that it only contains ATGC.
 // Returns true if this is DNA (ATGC only),
 // false otherwise.
 func CheckIsDNA(input string) bool {
    // Convert input to uppercase
    input = s.ToUpper(input)
    // If any character is not ATCG, fail
    for _, c := range input {
        if c!='A' && c!='T' && c!='C' && c!='G' {
            return false
        }
    }
    // If we made it here, everything's gravy!
    return true
 }
 // Convert a DNA string into four bitmasks:
 // one each for ATGC. That is, for the DNA
 // string AATCCGCT, it would become:
 //
 // bitmask[A] = 11000000
 // bitmask[T] = 00100001
 // bitmask[C] = 00011010
 // bitmask[G] = 00000100
 func DNA2Bitmasks(input string) (map[string][]bool,error) {
    // Convert input to uppercase
    input = s.ToUpper(input)
    // Allocate space for the map
    m := make(map[string][]bool)
    // Start by checking whether we have DNA
    if CheckIsDNA(input)==false {
        err := fmt.Sprintf("Error: input string was not DNA. Only characters ATCG are allowed, you had %s",input)
        return m, errors.New(err)
    }
    // Important: we want to iterate over the
    // DNA string ONCE and only once. That means
    // we need to have the bit vectors initialized
    // already, and as we step through the DNA 
    // string, we access the appropriate index
    // of the appropriate bit vector and set 
    // it to true.
    m["A"] = make([]bool, len(input))
    m["T"] = make([]bool, len(input))
    m["C"] = make([]bool, len(input))
    m["G"] = make([]bool, len(input))
    // To begin with, every bit vector is false.
    for i,c := range input {
        cs := string(c)
        // Get the corresponding bit vector - O(1)
        bitty := m[cs]
        // Flip to true for this position - O(1)
        bitty[i] = true
    }
    return m,nil
 }
 // Convert four bitmasks (one each for ATGC) 
 // into a DNA string.
 func Bitmasks2DNA(bitmasks map[string][]bool) (string,error) {
    // Verify ATGC keys are all present
    _,Aok := bitmasks["A"]
    _,Tok := bitmasks["T"]
    _,Gok := bitmasks["G"]
    _,Cok := bitmasks["C"]
    if !(Aok && Tok && Gok && Cok) {
        err := fmt.Sprintf("Error: input bitmask was missing one of: ATGC (Keys present? A: %t, T: %t, G: %t, C: %t",Aok,Tok,Gok,Cok)
        return "", errors.New(err)
    }
    // Hope that all bitmasks are the same size
    size := len(bitmasks["A"])
    // Make a rune array that we'll turn into 
    // a string for our final return value
    dna := make([]rune,size)
    // Iterate over the bitmask, using only 
    // the index and not the mask value itself
    for i, _ := range bitmasks["A"] {
        if bitmasks["A"][i] == true {
            dna[i] = 'A'
        } else if bitmasks["T"][i] == true {
            dna[i] = 'T'
        } else if bitmasks["G"][i] == true {
            dna[i] = 'G'
        } else if bitmasks["C"][i] == true {
            dna[i] = 'C'
        }
    }
    return string(dna),nil
 }
 // Given a DNA input string, find the
 // complement. The complement swaps
 // Gs and Cs, and As and Ts.
 func Complement(input string) (string,error) {
    // Convert input to uppercase
    input = s.ToUpper(input)
    // Start by checking whether we have DNA
    if CheckIsDNA(input)==false {
        return "", errors.New(fmt.Sprintf("Error: input string was not DNA. Only characters ATCG are allowed, you had %s",input))
    }
    m,_ := DNA2Bitmasks(input)
    // Swap As and Ts
    newT := m["A"]
    newA := m["T"]
    m["T"] = newT
    m["A"] = newA
    // Swap Cs and Gs
    newG := m["C"]
    newC := m["G"]
    m["G"] = newG
    m["C"] = newC
    output,_ := Bitmasks2DNA(m)
    return output,nil
 }
 // Given a DNA input string, find the
 // reverse complement. The complement
 // swaps Gs and Cs, and As and Ts.
 // The reverse complement reverses that.
 func ReverseComplement(input string) (string,error) {
    // Convert input to uppercase
    input = s.ToUpper(input)
    // Start by checking whether we have DNA
    if CheckIsDNA(input)==false {
        err := fmt.Sprintf("Error: input string was not DNA. Only characters ATCG are allowed, you had %s",input)
        return "", errors.New(err)
    }
    comp,_ := Complement(input)
    revcomp := ReverseString(comp)
    return revcomp,nil
 }
 ////////////////////////////////
 // BA1D
 // Given a large string (genome) and a string (pattern),
 // find the zero-based indices where pattern occurs in genome.
 func FindOccurrences(pattern, genome string) ([]int,error) {
    locations := []int{}
    slots := len(genome)-len(pattern)+1
    if slots<1 {
        // pattern is longer than genome
        return locations,nil
    }
    // Loop over each character,
    // saving the position if it
    // is the start of pattern
    for i:=0; i<slots; i++ {
        start := i
        end := i+len(pattern)
        if genome[start:end]==pattern {
            locations = append(locations,i)
        }
    }
    return locations,nil
 }
 ////////////////////////////////
 // BA1E
 // Find k-mers (patterns) of length k occuring at least
 // t times over an interval of length L in a genome. 
 func FindClumps(genome string, k, L, t int) ([]string,error) {
    // Algorithm:
    // allocate a list of kmers
    // for each possible position of L window,
    //   feed string L to KmerHistogram()
    //   save any kmers with frequency > t
    // return master list of saved kmers
    L_slots := len(genome)-L+1
    // Set kmers
    kmers := map[string]bool{}
    // List kmers
    kmers_list := []string{}
    // Loop over each possible window of length L
    for iL:=0; iL<L_slots; iL++ {
        // Grab this portion of the genome
        winstart := iL
        winend := iL+L
        genome_window := genome[winstart:winend]
        // Get the number of kmers that occur more 
        // frequently than t times
        new_kmers,err := MoreFrequentThanNKmers(genome_window,k,t)
        if err!=nil {
            return kmers_list,err
        }
        // Add these to the set kmers
        for _,new_kmer := range new_kmers {
            kmers[new_kmer] = true
        }
    }
    for k := range kmers {
        kmers_list = append(kmers_list,k)
    }
    sort.Strings(kmers_list)
    return kmers_list,nil
 }
 ////////////////////////////////
 // BA1F
 // The skew of a genome is the difference between
 // the number of G and C codons that have occurred
 // cumulatively in a given strand of DNA.
 // This function computes the positions in the genome
 // at which the cumulative skew is minimized.
 func MinSkewPositions(genome string) ([]int,error) {
    n := len(genome)
    cumulative_skew := make([]int,n+1)
    // Get C/G bitmasks
    bitmasks,err := DNA2Bitmasks(genome)
    if err!=nil {
        return cumulative_skew,err
    }
    c := bitmasks["C"]
    g := bitmasks["G"]
    // Init
    cumulative_skew[0] = 0
    // Make space to keep track of the 
    // minima we have encountered so far
    min := 999
    min_skew_ix := []int{}
    // At each position, compute the next skew value.
    // We need two indices b/c for a genome of size N,
    // the cumulative skew array index is of size N+1.
    for i,ibit:=1,0; i<=n; i,ibit=i+1,ibit+1 {
        var next int
        // Next skew value
        if c[ibit] {
            // C -1
            next = -1
        } else if g[ibit] {
            // G +1
            next = 1
        } else {
            next = 0
        }
        cumulative_skew[i] = cumulative_skew[i-1] + next
        if cumulative_skew[i] < min {
            // New min and min_skew
            min = cumulative_skew[i]
            min_skew_ix = []int{i}
        } else if cumulative_skew[i] == min {
            // Additional min and min_skew
            min_skew_ix = append(min_skew_ix,i)
        }
    }
    return min_skew_ix,nil
 }
 ////////////////////////////////
 // BA1G
 // Compute the Hamming distance between
 // two strings. The Hamming distance is
 // defined as the number of characters
 // different between two strings.
 func HammingDistance(p, q string) (int,error) {
    // Technically a Hamming distance when
    // one string is empty would be 0, but
    // we will throw an error instead.
    if len(p)==0 || len(q)==0 {
        err := fmt.Sprintf("Error: HammingDistance: one or more arguments had length 0. len(p) = %d, len(q) = %d",len(p),len(q))
        return -1,errors.New(err)
    }
    // Get longest length common to both
    var m int
    if len(p)>len(q) {
        m = len(q)
    } else {
        m = len(p)
    }
    // Accumulate distance
    dist := 0
    for i:=0; i<m; i++ {
        if p[i]!=q[i] {
            dist += 1
        }
    }
    return dist,nil
 }
 ////////////////////////////////
 // BA1H
 // Given a large string (text) and a string (pattern),
 // find the zero-based indices where we have an occurrence
 // of pattern or a string with Hamming distance d or less
 // from pattern.
 func FindApproximateOccurrences(pattern, text string, d int) ([]int,error) {
    locations := []int{}
    slots := len(text)-len(pattern)+1
    if slots<1 {
        // pattern is longer than genome
        return locations,nil
    }
    // Loop over each character,
    // saving the position if it
    // is the start of pattern
    for i:=0; i<slots; i++ {
        start := i
        end := i+len(pattern)
        poss_approx_pattern := text[start:end]
        hamm,_ := HammingDistance(poss_approx_pattern,pattern)
        if hamm<=d {
            locations = append(locations,i)
        }
    }
    return locations,nil
 }
--- a/chapter01/todo.md
+++ b/chapter01/todo.md
@ -1,21 +0,0 @@
 https://github.com/moul/euler
 - use snakemake
 main.go is a cli:
 - given a problem...
 - print url for problem
 - duration
 - answer
 - awesome go
 ba1c test
 - not testing everything
 - finish
 code coverage
 - https://mlafeldt.github.io/blog/test-coverage-in-go/
 - go lint
 - go test
--- a/chapter01/utils.go
+++ b/chapter01/utils.go
@ -1,95 +0,0 @@
 package main
 import (
    "bufio"
    "fmt"
    "os"
 )
 // readLines reads a whole file into memory
 // and returns a slice of its lines.
 func readLines(path string) ([]string, error) {
    file, err := os.Open(path)
    if err != nil {
        return nil, err
    }
    defer file.Close()
    var lines []string
    scanner := bufio.NewScanner(file)
    buf := make([]byte, 2)
    // This is awkward.
    // Scanners aren't good for big files,
    // just simple stuff.
    BIGNUMBER := 90000
    scanner.Buffer(buf, BIGNUMBER)
    for scanner.Scan() {
        lines = append(lines, scanner.Text())
    }
    return lines, scanner.Err()
 }
 // writeLines writes the lines to the given file.
 func writeLines(lines []string, path string) error {
    file, err := os.Create(path)
    if err != nil {
        return err
    }
    defer file.Close()
    w := bufio.NewWriter(file)
    for _, line := range lines {
        fmt.Fprintln(w, line)
    }
    return w.Flush()
 }
 // Utility function: check if two string arrays/array slices
 // are equal. This is necessary because of squirrely
 // behavior when comparing arrays (of type [1]string)
 // and slices (of type []string).
 func EqualStringSlices(a, b []string) bool {
    if len(a)!=len(b) {
        return false
    }
    for i:=0; i<len(a); i++ {
        if a[i] != b[i] {
            return false
        }
    }
    return true
 }
 // Utility function: check if two boolean arrays/array slices
 // are equal. This is necessary because of squirrely
 // behavior when comparing arrays (of type [1]bool)
 // and slices (of type []bool).
 func EqualBoolSlices(a, b []bool) bool {
    if len(a)!=len(b) {
        return false
    }
    for i:=0; i<len(a); i++ {
        if a[i] != b[i] {
            return false
        }
    }
    return true
 }
 // Utility function: check if two int arrays/array slices
 // are equal.
 func EqualIntSlices(a, b []int) bool {
    if len(a)!=len(b) {
        return false
    }
    for i:=0; i<len(a); i++ {
        if a[i] != b[i] {
            return false
        }
    }
    return true
 }
--- a/chapter1/Readme.md
+++ b/chapter1/Readme.md
@ -0,0 +1,69 @@
 # Rosalind Chapter 1
 This folder contains the `chapter1` module, which 
 provides functions for each of the problems from
 Chapter 1 of Rosalind.info's Bionformatics Textbook
 track.
 ## How to run
 * Each problem has its own function (example: `BA1a(...)`)
 * 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:
  `BA1a("rosalind_ba1a.txt")`
 ## Quick Start
 To use the functions in this package, start by installing it:
 ```
 go get github.com/charlesreid1/go-rosalind/chapter1
 ```
 Once you have installed the `chapter1` package,
 you can import it, then call the function for whichever 
 Rosalind.info problem you want to solve from Chapter 1:
 ```
 package main
 import (
    rch1 "github.com/charlesreid1/go-rosalind/chapter1"
 )
 func main() {
    rch1.BA1a("rosalind_ba1a.txt")
 }
 ```
 ## Examples
 See `chapter1_test.go` for examples.
 ## Tests
 To run tests of all Chapter 1 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 ./chapter1/...
 ```
 Note that this solves every problem in
 Chapter 1 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.)
--- a/chapter1/ba1a.go
+++ b/chapter1/ba1a.go
@ -0,0 +1,55 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1a: Most Frequent k-mers
 // Describe the problem
 func BA1aDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1a:",
 		"Most Frequest k-mers",
 		"",
 		"Given an input string and a length k,",
 		"report the k-mer or k-mers that occur",
 		"most frequently.",
 		"",
 		"URL: http://rosalind.info/problems/ba1a/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem,
 // print the name of the input file,
 // print the output/result
 func BA1a(filename string) {
 	BA1aDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	var input, pattern string
 	input = lines[0]
 	pattern = lines[1]
 	result := rosa.PatternCount(input, pattern)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(result)
 }
--- a/chapter1/ba1b.go
+++ b/chapter1/ba1b.go
@ -0,0 +1,59 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1b: Most Frequent k-mers
 // Describe the problem
 func BA1bDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1b:",
 		"Most Frequest k-mers",
 		"",
 		"Given an input string and a length k,",
 		"report the k-mer or k-mers that occur",
 		"most frequently.",
 		"",
 		"URL: http://rosalind.info/problems/ba1b/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1b(filename string) {
 	BA1bDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	k_str := lines[1]
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion: %v", err)
 	}
 	mfks, _ := rosa.MostFrequentKmers(input, k)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(mfks, " "))
 }
--- a/chapter1/ba1c.go
+++ b/chapter1/ba1c.go
@ -0,0 +1,51 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1c: Find the Reverse Complement of a String
 // Describe the problem
 func BA1cDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1c:",
 		"Find the Reverse Complement of a String",
 		"",
 		"Given a DNA input string,",
 		"find the reverse complement",
 		"of the DNA string.",
 		"",
 		"URL: http://rosalind.info/problems/ba1c/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1c(filename string) {
 	BA1cDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	result, _ := rosa.ReverseComplement(input)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(result)
 }
--- a/chapter1/ba1d.go
+++ b/chapter1/ba1d.go
@ -0,0 +1,61 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1d: Find all occurrences of pattern in string
 // Describe the problem
 func BA1dDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1d:",
 		"Find all occurrences of pattern in string",
 		"",
 		"Given a string input (genome) and a substring (pattern),",
 		"return all starting positions in the genome where the",
 		"pattern occurs in the genome.",
 		"",
 		"URL: http://rosalind.info/problems/ba1d/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1d(filename string) {
 	BA1dDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	pattern := lines[0]
 	genome := lines[1]
 	// Result is a slice of ints
 	locs, _ := rosa.FindOccurrences(pattern, genome)
 	// Convert to a slice of strings for easier printing
 	locs_str := make([]string, len(locs))
 	for i, j := range locs {
 		locs_str[i] = strconv.Itoa(j)
 	}
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(locs_str, " "))
 }
--- a/chapter1/ba1e.go
+++ b/chapter1/ba1e.go
@ -0,0 +1,59 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1e: Find patterns forming clumps in a string
 // Describe the problem
 func BA1eDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1e:",
 		"Find patterns forming clumps in a string",
 		"",
 		"A clump is characterized by integers L and t",
 		"if there is an interval in the genome of length L",
 		"in which a given pattern occurs t or more times.",
 		"",
 		"URL: http://rosalind.info/problems/ba1e/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1e(filename string) {
 	BA1eDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	genome := lines[0]
 	params_str := lines[1]
 	params_slice := strings.Split(params_str, " ")
 	k, _ := strconv.Atoi(params_slice[0])
 	L, _ := strconv.Atoi(params_slice[1])
 	t, _ := strconv.Atoi(params_slice[2])
 	patterns, _ := rosa.FindClumps(genome, k, L, t)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(patterns, " "))
 }
--- a/chapter1/ba1f.go
+++ b/chapter1/ba1f.go
@ -0,0 +1,61 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1f: Find positions in a gene that minimizing skew
 // Describe the problem
 func BA1fDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1f:",
 		"Find positions in a gene that minimize skew",
 		"",
 		"The skew of a genome is defined as the difference",
 		"between the number of C codons and the number of G",
 		"codons. Given a DNA string, this function should",
 		"compute the cumulative skew for each position in",
 		"the genome, and report the indices where the skew",
 		"value is minimzed.",
 		"",
 		"URL: http://rosalind.info/problems/ba1f/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1f(filename string) {
 	BA1fDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	genome := lines[0]
 	minskew, _ := rosa.MinSkewPositions(genome)
 	minskew_str := make([]string, len(minskew))
 	for i, j := range minskew {
 		minskew_str[i] = strconv.Itoa(j)
 	}
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(minskew_str, " "))
 }
--- a/chapter1/ba1g.go
+++ b/chapter1/ba1g.go
@ -0,0 +1,53 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1g: Find Hamming distance between two DNA strings
 // Describe the problem
 func BA1gDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1g:",
 		"Find Hamming distance between two DNA strings",
 		"",
 		"The Hamming distance between two strings HammingDistance(p,q)",
 		"is the number of characters different between the two",
 		"strands. This program computes the Hamming distance",
 		"between two strings.",
 		"",
 		"URL: http://rosalind.info/problems/ba1g/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1g(filename string) {
 	BA1gDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	p := lines[0]
 	q := lines[1]
 	hamm, _ := rosa.HammingDistance(p, q)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(hamm)
 }
--- a/chapter1/ba1h.go
+++ b/chapter1/ba1h.go
@ -0,0 +1,66 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1h: Find approximate occurrences of pattern in string
 // Describe the problem
 func BA1hDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1h:",
 		"Find approximate occurrences of pattern in string",
 		"",
 		"Given a string Text and a string Pattern, and a maximum",
 		"Hamming distance d, return all locations in Text where",
 		"there is an approximate match with Pattern (i.e., a pattern",
 		"with a Hamming distance from Pattern of d or less).",
 		"",
 		"URL: http://rosalind.info/problems/ba1h/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1h(filename string) {
 	BA1hDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	pattern := lines[0]
 	text := lines[1]
 	d_str := lines[2]
 	d, _ := strconv.Atoi(d_str)
 	approx, _ := rosa.FindApproximateOccurrences(pattern, text, d)
 	approx_str := make([]string, len(approx))
 	for i, j := range approx {
 		approx_str[i] = strconv.Itoa(j)
 		if err != nil {
 			log.Fatalf("Error: conversion from int to string: %v", err)
 		}
 	}
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(approx_str, " "))
 }
--- a/chapter1/ba1i.go
+++ b/chapter1/ba1i.go
@ -0,0 +1,70 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1i: Most Frequent Words with Mismatches
 // Describe the problem
 func BA1iDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1i:",
 		"Most Frequent Words with Mismatches",
 		"",
 		"Given an input string and a maximum allowable",
 		"Hamming distance d, report the most frequent",
 		"kmer that either occurs or whose Hamming neighbors",
 		"occur most frequently.",
 		"",
 		"URL: http://rosalind.info/problems/ba1i/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1i(filename string) {
 	BA1iDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	params := strings.Split(lines[1], " ")
 	if len(params) < 1 {
 		log.Fatalf("Error splitting second line: only found 0-1 tokens")
 	}
 	k_str, d_str := params[0], params[1]
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for parameter k: %v", err)
 	}
 	d, err := strconv.Atoi(d_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for parameter d: %v", err)
 	}
 	mfks_mis, _ := rosa.MostFrequentKmersMismatches(input, k, d)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(mfks_mis, " "))
 }
--- a/chapter1/ba1j.go
+++ b/chapter1/ba1j.go
@ -0,0 +1,71 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1j: Most Frequent Words with Mismatches and Reverse Complements
 // Describe the problem
 func BA1jDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1j:",
 		"Most Frequent Words with Mismatches and Reverse Complements",
 		"",
 		"Given an input string and a maximum allowable",
 		"Hamming distance d, report the most frequent",
 		"kmer that either occurs or whose Hamming neighbors",
 		"occur most frequently in the input string and in the",
 		"reverse complement of the input string.",
 		"",
 		"URL: http://rosalind.info/problems/ba1j/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1j(filename string) {
 	BA1jDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	params := strings.Split(lines[1], " ")
 	if len(params) < 1 {
 		log.Fatalf("Error splitting second line: only found 0-1 tokens")
 	}
 	k_str, d_str := params[0], params[1]
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for parameter k: %v", err)
 	}
 	d, err := strconv.Atoi(d_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for parameter d: %v", err)
 	}
 	mfks_mis, _ := rosa.MostFrequentKmersMismatchesRevComp(input, k, d)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(mfks_mis, " "))
 }
--- a/chapter1/ba1k.go
+++ b/chapter1/ba1k.go
@ -0,0 +1,62 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1k: Generate Frequency Array
 // Describe the problem
 func BA1kDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1k:",
 		"Generate Frequency Array",
 		"",
 		"Given an integer k, generate the frequency array of",
 		"an input string. The frequency array is an array of",
 		"counts with one count per index, and integers mapped",
 		"to kmers.",
 		"",
 		"URL: http://rosalind.info/problems/ba1k/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1k(filename string) {
 	BA1kDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	k_str := lines[1]
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for parameter k: %v", err)
 	}
 	arr, _ := rosa.FrequencyArray(input, k)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	for _, e := range arr {
 		fmt.Print(e, " ")
 	}
 	//fmt.Println(strings.Join(arr, " "))
 }
--- a/chapter1/ba1lima.go
+++ b/chapter1/ba1lima.go
@ -0,0 +1,51 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1L: Pattern to Number
 // Describe the problem
 func BA1LDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1L:",
 		"Pattern to Number",
 		"",
 		"Given an input kmer of length k, convert it to",
 		"an integer corresponding to its lexicographic",
 		"order among kmers of length k.",
 		"",
 		"URL: http://rosalind.info/problems/ba1l/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1L(filename string) {
 	BA1LDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	number, _ := rosa.PatternToNumber(input)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(number)
 }
--- a/chapter1/ba1m.go
+++ b/chapter1/ba1m.go
@ -0,0 +1,62 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1m: Pattern to Number
 // Describe the problem
 func BA1mDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1m:",
 		"Number to Pattern",
 		"",
 		"Given an integer and a kmer length k, convert",
 		"the integer to its corresponding kmer.",
 		"",
 		"URL: http://rosalind.info/problems/ba1m/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1m(filename string) {
 	BA1mDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	number_str := lines[0]
 	k_str := lines[1]
 	number, err := strconv.Atoi(number_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for number: %v", err)
 	}
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for k: %v", err)
 	}
 	result, _ := rosa.NumberToPattern(number, k)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(result)
 }
--- a/chapter1/ba1n.go
+++ b/chapter1/ba1n.go
@ -0,0 +1,60 @@
 package rosalindchapter1
 import (
 	"fmt"
 	"log"
 	"strconv"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Rosalind: Problem BA1n: Calculating d-Neighborhood of String
 // Describe the problem
 func BA1nDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA1n:",
 		"Calculating d-Neighborhood of String",
 		"",
 		"Given an input string of DNA and a Hamming",
 		"distance d, compute all DNA strings that",
 		"are a Hamming distance of up to d away.",
 		"",
 		"URL: http://rosalind.info/problems/ba1n/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Describe the problem, and call the function
 func BA1n(filename string) {
 	BA1nDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("Error: rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	input := lines[0]
 	d_str := lines[1]
 	d, err := strconv.Atoi(d_str)
 	if err != nil {
 		log.Fatalf("Error: string to int conversion for d: %v", err)
 	}
 	result, _ := rosa.VisitHammingNeighbors(input, d)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	for _, j := range result {
 		fmt.Println(j)
 	}
 }
--- a/chapter1/chapter1_test.go
+++ b/chapter1/chapter1_test.go
@ -0,0 +1,20 @@
 package rosalindchapter1
 import "testing"
 func TestChapter01(t *testing.T) {
 	BA1a("for_real/rosalind_ba1a.txt")
 	BA1b("for_real/rosalind_ba1b.txt")
 	BA1c("for_real/rosalind_ba1c.txt")
 	BA1d("for_real/rosalind_ba1d.txt")
 	BA1e("for_real/rosalind_ba1e.txt")
 	BA1f("for_real/rosalind_ba1f.txt")
 	BA1g("for_real/rosalind_ba1g.txt")
 	BA1h("for_real/rosalind_ba1h.txt")
 	BA1i("for_real/rosalind_ba1i.txt")
 	BA1j("for_real/rosalind_ba1j.txt")
 	BA1k("for_real/rosalind_ba1k.txt")
 	BA1L("for_real/rosalind_ba1l.txt")
 	BA1m("for_real/rosalind_ba1m.txt")
 	BA1n("for_real/rosalind_ba1n.txt")
 }
--- a/chapter01/for_real/rosalind_ba1a.txt
+++ b/chapter01/for_real/rosalind_ba1a.txt
--- a/chapter01/for_real/rosalind_ba1b.txt
+++ b/chapter01/for_real/rosalind_ba1b.txt
--- a/chapter01/for_real/rosalind_ba1c.txt
+++ b/chapter01/for_real/rosalind_ba1c.txt
--- a/chapter01/for_real/rosalind_ba1d.txt
+++ b/chapter01/for_real/rosalind_ba1d.txt
--- a/chapter01/for_real/rosalind_ba1e.txt
+++ b/chapter01/for_real/rosalind_ba1e.txt
--- a/chapter01/for_real/rosalind_ba1f.txt
+++ b/chapter01/for_real/rosalind_ba1f.txt
--- a/chapter01/for_real/rosalind_ba1g.txt
+++ b/chapter01/for_real/rosalind_ba1g.txt
--- a/chapter01/for_real/rosalind_ba1h.txt
+++ b/chapter01/for_real/rosalind_ba1h.txt
--- a/chapter1/for_real/rosalind_ba1i.txt
+++ b/chapter1/for_real/rosalind_ba1i.txt
@ -0,0 +1,2 @@
 CAGTGTAAGTAACGGATTGAGGACGTAACGGACTAGTATTCGAGGACAGTGTAATTGAGGACGTAACGGAGTAACGGATCGAGGACTAGTATCAGTGTAATTGAGGACGTAACGGAGTAACGGACAGTGTAACAGTGTAACTAGTATGTAACGGACAGTGTAAGTAACGGAGTAACGGAGTAACGGATCGAGGATTGAGGACCTAGTATCTAGTATTCGAGGATCGAGGATTGAGGACCTAGTATCTAGTATGTAACGGATTGAGGACTTGAGGACCTAGTATTCGAGGATCGAGGAGTAACGGACAGTGTAACAGTGTAATCGAGGATCGAGGACAGTGTAATTGAGGACTCGAGGACTAGTATTTGAGGACTCGAGGATTGAGGACGTAACGGAGTAACGGATCGAGGACTAGTATGTAACGGAGTAACGGACAGTGTAACTAGTATTTGAGGACCAGTGTAACAGTGTAACAGTGTAACAGTGTAACAGTGTAACTAGTATGTAACGGAGTAACGGATTGAGGACGTAACGGAGTAACGGATCGAGGATTGAGGACCTAGTATTTGAGGACGTAACGGATTGAGGACCTAGTATCTAGTATCAGTGTAACTAGTATGTAACGGATCGAGGATCGAGGACAGTGTAATTGAGGACTTGAGGACCAGTGTAATCGAGGATTGAGGACTTGAGGACTTGAGGACTCGAGGACAGTGTAAGTAACGGAGTAACGGATCGAGGACAGTGTAATTGAGGACCTAGTATTTGAGGACCTAGTATGTAACGGATTGAGGACCAGTGTAACTAGTATCTAGTATCTAGTATCAGTGTAATTGAGGACTCGAGGATTGAGGAC
 6 2
--- a/chapter1/for_real/rosalind_ba1j.txt
+++ b/chapter1/for_real/rosalind_ba1j.txt
@ -0,0 +1,2 @@
 TTACTCGCTGGCAGGTTGACGGAGAAATATTGGTGACGGAGAAGACGGAGAATGGGCATATATTGGTTGGCAGGTTTGGGCATTTACTCGCGACGGAGAATTACTCGCTGGGCATTTACTCGCTGGGCATTTACTCGCTGGCAGGTTTGGCAGGTTATATTGGTATATTGGTATATTGGTTGGGCATTTACTCGCGACGGAGAATGGCAGGTTGACGGAGAAGACGGAGAAATATTGGTTTACTCGCATATTGGTGACGGAGAAATATTGGTTTACTCGCTTACTCGCTGGGCATTGGGCATTGGCAGGTTGACGGAGAAGACGGAGAATTACTCGCATATTGGTTTACTCGCGACGGAGAATTACTCGCATATTGGTGACGGAGAAGACGGAGAATTACTCGCTGGCAGGTTTGGGCATTGGGCATTTACTCGCTGGCAGGTTTGGGCATTGGCAGGTTGACGGAGAAGACGGAGAATGGCAGGTTTGGCAGGTTTGGCAGGTTTGGCAGGTTTGGGCATGACGGAGAATTACTCGCTGGCAGGTTTTACTCGCTGGCAGGTTTTACTCGCATATTGGTTGGCAGGTTTTACTCGCTTACTCGCTTACTCGCGACGGAGAAGACGGAGAAATATTGGTATATTGGTATATTGGTTGGCAGGTTTGGCAGGTTTGGCAGGTTATATTGGTTTACTCGCTTACTCGCATATTGGTTGGCAGGTTTGGGCATTGGCAGGTTTGGCAGGTTGACGGAGAATGGCAGGTTGACGGAGAAGACGGAGAATGGGCATTGGGCATGACGGAGAATGGCAGGTT
 5 3
--- a/chapter1/for_real/rosalind_ba1k.txt
+++ b/chapter1/for_real/rosalind_ba1k.txt
@ -0,0 +1,2 @@
 CAATGAGTGATATTGTTTGGTAGCAATCCATAGTTGAGGCCCTACGGAAGTTGCATCCGGGGCCCGTAGGACTCGCGGGCAAAAGATTGCTAAGCATTCTTGGTCACCATCGCAGTATTGCTCGTAGTCGGGTGGGTTTGCCGAACTGATAATGTGCCAGTCCCCGCGGAACCGGAATCAGGGCAACGGCTAGAGATACTCTCCGTGGGTCCTAAGTAGGAGGCTTGGGGCTGAGTGAGCAACCACTTACTCGAGTGTGTTGTTTTCTGTGCGTCCCCCGGGCGGTGTTCATTTAAGGATGACCGGGTGAGTAACCGAACAATTTTGTTGCCATGAAACGCGGCAATAACTCAATCTACCAGTACGGACAAATATAATGTTGGGCCCTTTTAGCTTAACGGACGTCGTCCCATTCTGACCTTAACTAAGACTATAAGGTAGGGGGTCAGATACGACACGGTCAGTAGGTGGATATACCGTGACAAATACCGGCACCTATGCTAATTGCGATTTGGAATGGAACGCGCCGAATACTTCGGATCATATCACCGTCCCTGTACTCGAAAGTTCTGCCACGAACAAGTCTCCTACTTGTGTCTTTTCTCACTGCGAAG
 5
--- a/chapter1/for_real/rosalind_ba1l.txt
+++ b/chapter1/for_real/rosalind_ba1l.txt
@ -0,0 +1 @@
 TGCCGTATTGACGAACACCGAGCCCTAAT
--- a/chapter1/for_real/rosalind_ba1m.txt
+++ b/chapter1/for_real/rosalind_ba1m.txt
@ -0,0 +1,2 @@
 6003
 9
--- a/chapter1/for_real/rosalind_ba1n.txt
+++ b/chapter1/for_real/rosalind_ba1n.txt
@ -0,0 +1,2 @@
 TGCCCTAG
 3
--- a/chapter1/utils.go
+++ b/chapter1/utils.go
@ -0,0 +1 @@
 package rosalindchapter1
--- a/chapter2/Readme.md
+++ b/chapter2/Readme.md
@ -0,0 +1,69 @@
 # 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.)
--- a/chapter2/ba2a.go
+++ b/chapter2/ba2a.go
@ -0,0 +1,67 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2a: Implement Motif Enumeration
 func BA2aDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2a:",
 		"Implement Motif Enumeration",
 		"",
 		"Given a collection of strings of DNA, find all motifs (kmers of length k and Hamming distance d from all DNA strings).",
 		"",
 		"URL: http://rosalind.info/problems/ba2a/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2a(filename string) {
 	BA2aDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("ReadLines: %v", err)
 	}
 	// Input file contents
 	params := strings.Split(lines[0], " ")
 	k, _ := strconv.Atoi(params[0])
 	d, _ := strconv.Atoi(params[1])
 	// 1 line in the input file is for
 	// parameters/gold standard.
 	// The rest of the lines are DNA strings.
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	results, _ := rosa.FindMotifs(dna, k, d)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(results, " "))
 }
--- a/chapter2/ba2b.go
+++ b/chapter2/ba2b.go
@ -0,0 +1,61 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2b: Find a Median String
 func BA2bDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2b:",
 		"Find a Median String",
 		"",
 		"Given a kmer length k and a set of strings of DNA, find the kmer(s) that minimize the L1 norm of the distance from it to all other DNA strings.",
 		"",
 		"URL: http://rosalind.info/problems/ba2b/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2b(filename string) {
 	BA2bDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	k_str := lines[0]
 	k, _ := strconv.Atoi(k_str)
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	results, _ := rosa.MedianString(dna, k)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(results)
 }
--- a/chapter2/ba2c.go
+++ b/chapter2/ba2c.go
@ -0,0 +1,54 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2c: Find a Profile-most Probable k-mer in a String
 func BA2cDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2c:",
 		"Find a Profile-most Probable k-mer in a String",
 		"",
 		"Given a profile matrix, find the most probable k-mer to generate the given DNA string.",
 		"",
 		"URL: http://rosalind.info/problems/ba2c/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2c(filename string) {
 	BA2cDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	dna := lines[0]
 	k_str := lines[1]
 	k, _ := strconv.Atoi(k_str)
 	// To make multidimensional slice,
 	// make a slice, then loop and make more slices
 	profile, _ := rosa.ReadMatrix32(lines[2:6], k)
 	// Find the most probable kmer
 	result, _ := rosa.ProfileMostProbableKmers(dna, k, profile)
 	fmt.Println(strings.Join(result, " "))
 }
--- a/chapter2/ba2d.go
+++ b/chapter2/ba2d.go
@ -0,0 +1,67 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2d: Implement GreedyMotifSearch
 func BA2dDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2d:",
 		"Implement GreedyMotifSearch",
 		"",
 		"Find a collection of motif strings using a greedy motif search. Return first-occurring profile-most probable kmer.",
 		"",
 		"URL: http://rosalind.info/problems/ba2d/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2d(filename string) {
 	BA2dDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	//// Input file contents
 	params := strings.Split(lines[0], " ")
 	k, _ := strconv.Atoi(params[0])
 	t, _ := strconv.Atoi(params[1])
 	// 1 line in the input file is for
 	// parameters.
 	// The rest of the lines are DNA strings.
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	result, _ := rosa.GreedyMotifSearchNoPseudocounts(dna, k, t)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(result, " "))
 }
--- a/chapter2/ba2e.go
+++ b/chapter2/ba2e.go
@ -0,0 +1,67 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2e: Implement GreedyMotifSearch with Pseudocounts
 func BA2eDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2e:",
 		"Implement GreedyMotifSearch with Pseudocounts",
 		"",
 		"Re-implement problem BA2d (greedy motif search) using pseudocounts, which avoid setting probabilities to an absolute value of zero.",
 		"",
 		"URL: http://rosalind.info/problems/ba2e/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2e(filename string) {
 	BA2eDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	params := strings.Split(lines[0], " ")
 	k, _ := strconv.Atoi(params[0])
 	t, _ := strconv.Atoi(params[1])
 	// 1 line in the input file is for
 	// parameters.
 	// The rest of the lines are DNA strings.
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	result, _ := rosa.GreedyMotifSearchPseudocounts(dna, k, t)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(result, " "))
 }
--- a/chapter2/ba2f.go
+++ b/chapter2/ba2f.go
@ -0,0 +1,64 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2f: Implement RandomizedMotifSearch with Pseudocounts
 func BA2fDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2f:",
 		"Implement RandomizedMotifSearch with Pseudocounts",
 		"",
 		"Re-implement problem BA2e (greedy motif search with pseudocounts) but use a random, instead of greedy, algorithm to pick motif kmers from each DNA string.",
 		"",
 		"URL: http://rosalind.info/problems/ba2f/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2f(filename string) {
 	BA2fDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	params := strings.Split(lines[0], " ")
 	k, _ := strconv.Atoi(params[0])
 	t, _ := strconv.Atoi(params[1])
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	n := 100
 	result, _ := rosa.ManyRandomMotifSearches(dna, k, t, n)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(result, "\n"))
 }
--- a/chapter2/ba2g.go
+++ b/chapter2/ba2g.go
@ -0,0 +1,65 @@
 package rosalindchapter2
 import (
 	"fmt"
 	"log"
 	"strconv"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA2g: Implement GibbsSampler
 func BA2gDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA2g:",
 		"Implement GibbsSampler",
 		"",
 		"Generate probabilities of each kmer in a DNA string using its profile. Use these to assemble a list of probabilities. GibbsSampler uses this random number generator to generate a random k-mer.",
 		"",
 		"URL: http://rosalind.info/problems/ba2g/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA2g(filename string) {
 	BA2gDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	params := strings.Split(lines[0], " ")
 	k, _ := strconv.Atoi(params[0])
 	t, _ := strconv.Atoi(params[1])
 	// Make space for DNA strings
 	dna := make([]string, len(lines)-1)
 	iLstart := 1
 	iLend := len(lines)
 	// Two counters:
 	// one for the line index (iL),
 	// one for the array index (iA).
 	for iA, iL := 0, iLstart; iL < iLend; iA, iL = iA+1, iL+1 {
 		dna[iA] = lines[iL]
 	}
 	n := 100
 	n_starts := 20
 	result, _ := rosa.ManyGibbsSamplers(dna, k, t, n, n_starts)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(strings.Join(result, "\n"))
 }
--- a/chapter2/chapter2_test.go
+++ b/chapter2/chapter2_test.go
@ -0,0 +1,13 @@
 package rosalindchapter2
 import "testing"
 func TestChapter02(t *testing.T) {
 	//BA2a("for_real/rosalind_ba2a.txt")
 	//BA2b("for_real/rosalind_ba2b.txt")
 	//BA2c("for_real/rosalind_ba2c.txt")
 	//BA2d("for_real/rosalind_ba2d.txt")
 	//BA2e("for_real/rosalind_ba2e.txt")
 	//BA2f("for_real/rosalind_ba2f.txt")
 	BA2g("for_real/rosalind_ba2g.txt")
 }
--- a/chapter2/for_real/rosalind_ba2a.txt
+++ b/chapter2/for_real/rosalind_ba2a.txt
@ -0,0 +1,11 @@
 5 1
 GATTTGGGCCAAAGTCTGCGGCGAA
 GATGTGCGTCAACCAGTCGGAGTCC
 TCACACCGGCTCGGAGATTTTTTTT
 GATCTACAACGCGTGACTATATGCT
 TAAGTGATTTTGTGGCCTTTACTCG
 CCATCTACCCGATGTTCGACCGCGT
 GAGCGCGCTGCCTACATTTGGATCT
 TCCGGGTTAGGATGTTGAAACAAAA
 ATGGAGCCATGATATGTACACTTAG
 GCATGGATCTTACTCCGACGTTATC
--- a/chapter2/for_real/rosalind_ba2b.txt
+++ b/chapter2/for_real/rosalind_ba2b.txt
@ -0,0 +1,11 @@
 6
 CCCTAGTCTACCTGTTTGGAGCGGGGCCTGAATTTGACTGGC
 GTCTTTACCGAGTTAGTCTGATGTAAGTACTGCTCCTCTACC
 CCGACATTGCGCTCTACTCTGCGCACATAACTAAACGTTGCA
 CCTCCGTCTACATAGAAGGAGTCTGCAACGCCCCCACTGAGG
 ATCTTGCTCGTATCTACCGATAAGTAGCGAAAATCTAGCGTT
 CGGGGTTACCTGGCAGTGTCTACTAGATCAGATTGCCCGGCT
 TTAGTAAATGAATCTACGTCTCTGAGCGCGCGAATCAGGGTG
 TGAGCACTCTGACTTAACTCTACTACTCTCCAATAAGCGCTC
 TCACGTTCTACACTAGGTAAGTATGCATATTTGCATGAGTCT
 TTTGAAGAAGGCTCTACAAATTTAAACCCAGACTCAGACACG
--- a/chapter2/for_real/rosalind_ba2c.txt
+++ b/chapter2/for_real/rosalind_ba2c.txt
@ -0,0 +1,6 @@
 GTCACAGCTGCATAACAAGTAAACTGAGAAATCCCCAGTTAGGCGGATTGACCATCGAACACACTTTCACTACTTGCGGATAAATCCTGTAGAACTAGACTTTATCTCGGCTGCGACAAGACAGGAGTTCATGCACCTGCTCTGTCCCTCGCAACAGTCTAGGGAGCAAGTAGGCGGCTTCTTAGCTAGTACCTGGGTAG
 7
 0.393 0.286 0.286 0.25 0.179 0.321 0.107
 0.071 0.357 0.25 0.286 0.214 0.393 0.357
 0.214 0.214 0.143 0.286 0.25 0.143 0.25
 0.321 0.143 0.321 0.179 0.357 0.143 0.286
--- a/chapter2/for_real/rosalind_ba2d.txt
+++ b/chapter2/for_real/rosalind_ba2d.txt
@ -0,0 +1,26 @@
 12 25
 AGATCCGGTTTTATTCAAGCGAATTAGTGGGAGTGCGAGCATGCGCCAGATTCGTCCGGGATTGTCGTTAGGACACTAAACAGAGTCAGGTGCAGTGAGGAACCGGTCCTCCTTGCTGTCCATCTTTGGCTATCAATCGCTTTGCGGGCGGCATGC
 CGAGCATCCCTTTAACATAATTGCCCGTGGGTGTATTGCGTTTTTCCAACGCATAAGAGCATCTTATGTGTTTATGCGTGGAAGCCTATCACTTTGCATAGCGTTTGGCGATCACCTCCATGCCGCAAGGCCTAAGGCACACGGTTAATTGGGTCA
 AACGAGGCGAACCCTGGAACAGGTACCATGCCTTTGCGATTCAGCTTCTATCCCCGTCTAATTAGACATCTCAGCGTTCCTCAAGCTAGCAGACTGCACAGGGCTTATCCCCGGATGGTCGCTACTTCTCTGTGCATATAGCACGTAATGCCACAT
 CTTCCCGTCGAAATGCTACATAGACTGAGCGATACATGCGGTGCAGTTAGTTTGTTGACCTTATCCCACACTACAACGGCCTGTTACATTGCGCGTGTCTTATGCAAATCGATCGCTTTGTAACCGTAATCCACCATTTCTGGAAAGCATTTCCAG
 ATTAAACATTCCAGCAACACGCGGGCGATCCTGAGGAATCACCGCAACTCACGTCTAGAGCCTGTCCGGCACTCGATTACTTTGTCTTTCGAACCCCGTTGGTTAGTGCACTCTGTCATATAGTGCTAGGCTGCCCTCTCAGACGCGCTCAGTCGT
 TCGGTGTGTACACCTGGTAGAGGAGGAACCAATTAAACTTCGTGAACCCAAGGCGGCCCCCCATTCAGTTCGACTGGGACTCCGGCGCTTTTATGCGCGCGTAGAGGCAGTGACAAGGCTTCCGGTTAAGTCTTCTTTACTGACGCCATGCCTTTG
 CGTATCTCTGTTTAGGCTCCCACCCCGATACCTTTGTTTCTCATATGAGCGCTTGTCTCGCCGCCAGATATCTGACTGGTCCGGTGATCAATGCTTAGGCGTTCAGGTTTACTACTGTCGCGACAAGACGGTCATACGCGCCAAAGGCTTCACAGC
 AAGCGAAGTCCTTTGAATACTAAAACTCACCACTGGGCCGTCCCGACTATAAGTTGTCGCGAACAGAGTTTCTGTTACTTACCTCACTATCTTGCATCCATTCCTTTGGGTATTTGGGTTGTACACGCTATACGATCATGATTAGTCTCTATGCCT
 TAACAACGATGCGGTTCCGTAATCGTAGTGAGAAAACCGGGTAGGAAGTAAGTGTGCATGAACGTTAGGCGCGTCTTGAAGCCAGATGGGTAGCTGGCTAATGTTTCTGCCATAGGACTGGATCACTTGTGCCCAACAGGAACAGCAATTCCTTTG
 GCGATGACTTTGACGGCAGATCCGACCTCGGCTTAGTATGGTGGATGAACCTCCAAGTCACCGGGTCCTAGCATTATTTCGAATGGCCGAGGAGGCCATCATTAGGTAACGCCCAGAGTACATCCCCCGAACACCGAAGGTCGTTCGCGTCCGGCA
 CCTAACGTACCATTTTTGACTGGAAGCCAAAGTTGACCGGCTTTTATAGCTTTTGACGGTCTCCTGTACTCAAGTAGATTTTTGTTAACAAACCTGGCATTGTCGTCATACAGTCAGGGAAGATACTTCCCTAGCTGCACCCACCCAATAGCTTTG
 TGCTCTGACCAGACGATGGCTTTGCTGGAGGTTGAAGGCCATTTTTTTGTTCTAGTGCCCGACAGCTTCATGAGGGCGGTCGACTCTGAGGCTTGAGCAAAACCTAATATAAATGCTGAAGCTTAGCGCACGGCACGGAAATTGGGGGGAACTACT
 CGGAAGCGTTTATGACGGCGACAGGAGTAACCATGAAGAGGAACAGGCGCGACGATGGAACCGCCTTACTACGTTCCGTCACGCCACCCGAGTGGAGTCGGTACCGTTAAGCTGACGGCGCGCTATTCTCTCCTGATTAGGTTACCTATGCCTTTG
 GATGTAGCCATATAAATCATTCATCGTTATTGTGGGCTCTTGTCTACCGTATACACACACCCAATCCCTTTGGGCATTATTCGACTATCCCCTACCTCGCCTACTGCTGATACCACGTTTTAGGCTCCGTTTCATATATATCCCCCTAAACAAGGG
 GATGGAGCGTTGGCGAACCGCTGAGCGAGCTATGAACAGCCTGTGAGACGCGGGGTAGGAGCCATCACTTTGGATCGTTCCCAGTCTTTCTATTATCAGTATCGATATGCGGCAACCAGTTTTCTTGCGCTCTGAACCATCCTATAGTAGAACTTC
 TCCTATACGTAGCCTCGTCCGGCCTGACGTGTCCGGATTCATTTAGAGGCCATTACTTTGCTGTCAGTCGCTGCACTCATGTCGATTGTCGTGGTTGATTTAAAGACCCGCATAGCACAGTACCCTAACCCCAACTTCTCTCTGTTTAGACAGTGC
 GAGCTTTGTATGGAGATTGCGCTTCCGATTGCTTTGAACATCGGACGCGCTTATAGAGACACTCGTGCTGGCAGACCGGTGCGCGATAAACGAATCTCGGCGTGCATTGGTGTTTGGGCTTCCGATGTCAAAGACCGCAGAACTGCGCCGGGGAAT
 CGATCTTCAAAGGCTGGCTTGCATTAGGAGGACTGTGAAGAACACGCTTCTCTTATGACTGCACGGCGGTTGACTACGTCGCTTTGGGGCCACCCTTTCATTGCATGAACAATACCTTTGGTCTTTGACTGATCTTGAGGAGTCCACCGGATCACT
 ACATTTCAAACACACTGTATGGGTTACCCTAATTCGCTGCGCATGCGCTGGGCCTCGAGCGAAGAATGTACGTGCTTTAGCTACTGTCAGTCTATCCAACGAAACTACGGCTTACGTGGTTACAGACCCCATGCTGGTTGGGAATCGATTTCTTTG
 TATAAAGAAGTAGGTCCGTCAGATTCGAGGAATCCTCGATGTCCCTGGTACATGCAAAAGTTCAGAGCCGTAGAACTACTGTAGGCGATTGCTTTGCGCAAAAGGGATCAGTCGCCGTCGTAACTCAAATTTAGTCTTTTCACCAACGTGCAGGGA
 TTTGAGTCATTATTAACGGTGTACGGAGTGACGCCCCCAATGCCTTTGTCCGGCTTGTACCGGATTATCCGCTTGAGTAACTTATTCTTATCTGAGATGTCGGTGGATATTGCCACTTAATCGAAACGATCGTACCTCGCCCGAGTCCTAGCAGCG
 CGCACGTGAATGTAGGAGCCAATCCGGCCTCTTTAGTGCTCCAATCACTAAGGGTAGATTTGTCGCACCACCCGTATGTGATCCCTCAAAGCGAAATCATCTACACTCTCCATAGCTTTGAAATCCAATAGTACAACCTCGGCCGGGTAATCACCA
 ACCATATCTTTGCGGACTTCCGAAAAGATCGAAAAAATAGCTTACTGACCCCCAACCTTGAGGTAAGAGCGGTCCCTCGGTCAGGCGGAACTTCCAGTGTCCGATTAGATCAGGCCGCATAGTGTGGGACTCCGATCAAGTGTATAATATGCAGGT
 GCGGGGGGAGTTTGCTAGGACAGTCGGGCGGTAGTTTGTGTCTTAAGTAACTGCTCGAAGGCTAGAATGTGGGATCATAGCTTCAGCGGATTCCTAGCGATGGCTTTGAAACATGGACGAGTTACTTTTGGCGTTTTTGAGAGTTTATAAGGTGAG
 CCAAACATGGTGGTCACTATTAATTGTCCTCCGCGTACCGAGATACGAGGGGAGTCCTCCCACAATTCGTCGCCGATTTCTTTGAGTCAGGGTATCATAGGGAGTGCTATTCCATAGCGATAACTGCTCCACAGAAGTTCATTAAGTATTTTTTCT
--- a/chapter2/for_real/rosalind_ba2e.txt
+++ b/chapter2/for_real/rosalind_ba2e.txt
@ -0,0 +1,26 @@
 12 25
 GATGTGCGTCACAATCCCGCCCTCCAGCTGAACTAGCCAATACTTCCTCTTTCTGCTTCATGATTCACCCAATAGACACTAGGGCTTATACGGGGTGTGTACTTCCCACTGTGGGGCGAGCTGAGTCCATAGTCATGGGCCCGCCTCATCTAAACC
 TCATAGCCGCCGCGCTGGTGGGTGCAAGTCTGCCGACTCCCACCTTATATGTAGCAGGTCACGTAGATAGGAGTGTGTTATATCCTCCGATAATCCCTAAATATAGGATGATACTGGTTCTGCCAGACTCTGTCTGTCTTGAAGTCGCTAGATGAA
 GCGTATAGAAGGAATCCGACTTGGACGCCATTCAGATCAACTAACATAAACAGCAGTAAGCACTTAGCTAGTTGATACCGACGCATACAGAGCGGTCGCGAAAGTCGAGACCGTTCCTTGGTTCAGCAATTCGTGGCTGCCGTCCTCTGGTAAGCC
 ATTGTATGGAACGGTGATGTGCTACTCGCTTAAACCTATAAGCGCACATTTGCAGTCCATGTGATACCTTCCAAGATGTTATTGGCGTGGAAATTAATAAGACGAGACTATTCGTCCTCTGGGTTAAGCTGGTATTTAGAAAGATTATCCAGCAAT
 CGGGCCGCAATGGGCGCCATTACGTTTTTGGTTTAATCATTGCTGGATCTCCCAACCCACTCGCCTGCGGGACGTTCGCTCAATCTCCGCCCACGTCTGTGCTCTATCTCAACGATAGTCCTCGACTATAGCCTCATGTAAACCCGGGAGACCTTT
 ACACAGCGCCTCGCAGGGGGTGTGAGGACCGACGTTGTAAAGGCCATACCGACTCTCAAGGCATTTTGGGAACCCCCACCTGTCTGTGCCATTGAACTCTACTAACCCTAATTCACCTATTGCCGAGCCTTCGGATTTGACGAATACGCATTGCGG
 AGCTAGCCGCTTGCCAAACCGCTCTCAGAAGGAACGAGCCTAATTCTCCTCACGTAATCCGGCCAGTTCATAGGTGTGCAAAAACTTAACACACGTTCGGGTGGGGTTAGCAGCGCAGAATTGAACCCCTTCACGCCGACAGGGTGGCTAACTACA
 ATTCATGATTGCTGAGTCATTGAAACACACCAGAAACGTCAGCGGCTAGACTATGTACCAGCGGAAGCTGGGATTCCTTTAGAAGCTGTTCCCATACTTGGTGGGTGATCCTATGATACTCTCGGTTAATCCGTGCGAATTTAGCTGTCCCTGAGT
 TGGTTGTGATATTAACCAAGTGCGCTCCCCTAAACCTCGAACCTGGGCCATTTAGATGACTTAACGCCGCCTAGCAGCGCCGCCGTGGTCTTACAACTAGATAGAACTGCGAGGCATTCTGCGGGGCGTAAGTGTCGTCACAGCGATCATGGATTC
 AACTTTCATGTCCACGCGCAACCTTCGGTTTCGTCCCTCTGCTAAACCAATTGGTCATTTCTATTGCTGGACCCACCCGCAGGCGGTCGAAAAGAAATACGCTGCCCCGAATACAGCTCCGATTCCTCTTGCCTCCCAGACACAGATGGTAACTTA
 GGTCCGCGTTGTAGTACACGTAAAGCCTTATCGGGGGTCCTAAATCTAGTACCTGGCAGACTCACATAAACCGCTCTCCCCGCCTGGAATCTAATGTCTGTAACTGATCCTTTTCCTTCATATCAATACCTCTGTATCAGTGTCCAAAGGTCAGCT
 AGATGAGGTGCAGTGGGGGGAGTGATGCTAAGTGGTCCCACTGAACTCATTGAACCCATACTCGGTGGGACTAACATCTACAGCCGCACGTCAGAACTACAAACAAGATCGGCACGAACGTTCGCGACTATTTACATCTTAGCGCTCTACTAATCC
 CGCGTTGTTGCCCCCGGATTACTACTCATAGTCTGGACAACTGAGACGATAGCTCATCATCGCGGTAACATGCGTGATTACGGGGAAAATTATGGGGTGACCCAGATCCGCTTCGACGCGCTCACCTAAGCCAACACGCGGGTATCGGTCTAGTAT
 TCTGACGCTTTCCCCACGAGAAGATCATCCCGGTTGTTACGATCCTTCCTCCAATAAACCTGCGCCCCATACTGAGCGGTACCCTTTCAAAGGTAGAGTGCTACCATGCGATGTATCTGAATACCATAAACGTGTGAGTAGGATTGTGGGGGTACA
 GACCGAAAATCGATGGCCAGACCCATCGAAGTCCGCCCCAAGTTGGCTATGAGTTTAATGTGCGCGTTGCTGCTATGAGGATGTCAGGCTGGGCCGAGGGAATGAGAAAGTTTCTGACCTCGAATGAGAGTGAGTCCTCCCGCACTCCGCTAAGCC
 TTAAGGTCTCTGACCGTTGTAAAAATTGTGCCCCCCCATCTTGTAATCGCTAACGAAAGGAAATCTTCTTGACAACCACAACGAGTAACTGCCGACTCGGTGGGTAGCCAGCGGTTGACGAACTGGACAATGCTCTAGTAAACCCCGGTCGACAGC
 TAAGAAACCTTGTCGACTGGGAAACTCGCGTAAACCTTTGCGGAGGCTCCTTATCGTTACCTGACTTCCAGAGGGACTACCGTCGAGTCAAGGGGTCAGTTAGGTAAGCACACGATGCATGCAACCCTTGCTGACTTCTTCAATTTCCGTGACCGT
 GACCATCAAGCCCGTAAATCGATGGTATCCTATGGTATCGTCACCACAGCCTCGTCACTTAAACCAGGCGTAAACCGAGTGAAACGACTCGGCTCGCAGATAGAACCCGTGTAGAAAACCATGTGAAACAAATGAATCACTTTACTCGGGTAAGCC
 TCAGTGTTAGCCTCGGGTCAGAACGGTCTATTGAAGTTAATGACACTCGGGTAGTCGGCGCTCAGCTAATCCGCCGCTAAGCCACGAGCAGGCGACAAAGGAGAATCTGGCGACGGGTAGCACGATAGTTGGGGAGGCCTCGCCTAGGTTAGACAG
 CTCGACTAATCCGAATTACACTGCACCTCCGAGTGGGTCTGGTTACTGCCGGTAGGGAGGCCAAATAGCTTGCCCAACTCGATAAGTCCTATGACGATCGGGCTGTCATAACAAGATTAATAGGGATGTCAAACCGTAGGGTGCACAGACAATTCC
 ATCCAATTCTCGATGGGATTACACCCTAACCAGACTGGGGATCCATAAGTCTTTTTGCCTCTCGCGTAATCCGCGCATGACTGTATACACTTCCCCAACGGGGGGTCAGTGTTTTCTATTCCCGCAGCACGCCCCGTCTAGCCGACCCGAAGGTGC
 GATGTCAGATTACACCATTTCTGGCGCGTTTTGAAAGATCGGACCTTCATATGGGTTCCTGCTCAGCGTGGACCAATGAGAATGGAGAGCCATGAATTAGCACTACGACTCTCCTAAACCATGATTCTGATTTTCTGATCTTCCCATCAGCCGTAC
 GCTAATCCTCCTGAGTTACGAGCATCCATGCGATAAACAAGACCGATTCACATCCAAATTGGCCGTCTCTGTGATGCTGGGCCGGTGAAGTTGACTTCGTAGAGTTTATCTCCAGCCTGCAACCTGAAGGATCTCGACTAACCCTTAAGCGAGCTG
 CCGCTCGAAGATCCCCTCTTGCAGCACGGTGCAGGTTCGGCAGGCTGAAGTCTACACCGCTTTGGTGACAAAGCGAATGACTCACTTAGGCCCGCGCATAGGGCAACCGTACATCACCGACAGAGTGTACAGCTCGGCTAAACCAGACATACGCTT
 GGGGAGCGGTGTCGAAAGAGAAGGCATCTCTGAAGGAGTTAAAAACCACGATTTGAAAGTCCTCTGTATATGCTCGCGTAAGCCTTGCTTTTCCCACTGAGGCTACACAGGCGAGTCCAGCTAATGACGGCGTTCTCATCTCAATGTTGGCGACTG
--- a/chapter2/for_real/rosalind_ba2f.txt
+++ b/chapter2/for_real/rosalind_ba2f.txt
@ -0,0 +1,21 @@
 15 20
 CCCCGAGTAATTCCCAGATATAACGTACTCAAATGTTGAAAACAAGTGACCACTGTATCCACGAGGGGTGTAACTCTTATCAATGGCATAAGGGCCACGAGGACTCTACCATAAGAGCACAGCGCCAGCTGACGAATGAGTATCTCTGACCAACCGATTGCGATCTGTTGTTGGCAGATAGGCCCGCAGGACCCCGAGTAATTCCC
 AGATATAACGTACTCAAATGTTGAAAACAAGTGACCACTGTATCCACGAGGGGTGTAACTCTTATCAATGGCATAAGGGCCACGAGGACTCTACCATAAGAGCACAGCGCCAGCTGACGAATGAGAGATTTGACTACTAGTATCTCTGACCAACCGATTGCGATCTGTTGTTGGCAGATAGGCCCGCAGGACCCCGAGTAATTCCC
 ATAGTGCGTACACCACAAGTGAGATATGATACTTCGACCCAGAGGTAAAGATAAGATCTAGTATTAACCCCGGAGCGAAGGGAGAATGGTACGATCTTGAACAGACTACTCATCGCCGATATGAGTCGAAGATAATGCTGTCATCAAAAGTGGCTTTGTTGAGGTTAACACTGTAGACTGGATGCAAGGCCGATGAATTATAAGTC
 CGGGCTCGGAGAACAGACTAGGGGTACGAAAAGGTTCCGAAATTAGCACGCGCGCGTATAAAAAGATCGACGACCATGCCCGAGTTAGCTCACAGGAACAACTTTGGATAGTTAGATCCCAGCTGACAGTTCGAACTACGCAATCAGGGCTCCTCTGGATTCATACTCTAAGCATGAGAAGGCACAGAGCAAACAGCTACTTGGAT
 CTTCAGTTAATGATGCCTCAGAGGTCGGCGTTGAACCGCGTAACAGACTACTATCTTTATGCGCAGTACAGTTGTAATATGACTAAGGCGCCCGCGAACCGTTCCAACGTGCCGAGAAGGTTGGCCTACAAGGAAGAAGCCGGTCATTCAGTCTTCAAGGCCAACGGTCCTGCACAGATGATTACGCACCGATCAGTATAATGTGT
 CCATTGGGTGAGTTGATTCCATGATTCGTAGAAGCCACTACTAGGTGAGCTAGGCTCCTCTACAGTATAGAGAAGAGCCTTTAAGCCTATCCTGGAGCCTCTCACCCCACAATCGTAAGAACTTGGGTGCGTGAATGACTGAAGTATACATCACCTTAACTCATATTGTTGATCCGCTGTTGTCTGATTGGTAGGCTTGGTAGCGC
 CGAGCGCTTTTTGCACACCGAACGTGTCAGTTCCACATGAGCGTGACAGAGTGCCCGCGCATGGGGTAATCCCGTATCAGAACAGTAAACTAGGTCATGTCCTCCATCGTCTTAGAAGGGGACAACCCCGCAGGGTATGCTAAGAAGTGGAGTAGAGAGTGTTGTGCTGAACACGCGTATCCGGCGGTTTCAAAGTCCAAGGTTGA
 TGTCGTCCCTCTTCTTTTCACTCACATGTATGCCGCTAATACAGACCAACTAAAGAAGAACCAGCTACTAGTGCCATACCTCAAAAGCTAGAACTGTAATAACACACCGCTCGTTGTGGGCCGATTGTATATTAGTAAAGCAGCCAATATTTGTAACACGGCCGATGACCGTGCAAGTTTCCCTTGGAGGCAATGGCATCAAATTC
 TGAGGTGATTGTTTATCCAGATTGGCTGTTTGTCTGAGAAGCTTGTAGCGAGATTCGACTACTAGCTATAGCGACTCAAAATGCTGCGCATTCCCAACTAAAGTAAAACGCAAGCTTAGATGCAGAATTGAGATCACTTGTCTGGATTCATTTTTAATGTGGCGCTACAGGTGCATGTCATGCCCGGTAGGTTGAGAGGCTCTCAA
 ACGTGGAGCGATCCTACCGGTGTATGTGTACCATCCTGGCTGAAAGGCAGTCGACTGGCCACCGTTCGGGCGGCTGCGTTAGAGCTGACTACTCGCATAGGTCTAGAGCGATGACCCCTTGTTTGTCAGCGTATATCCTGGGTAATCGTTGTACCGCCTTTCAGGCCGATCCTAGGCAAGACTACTAGAACTAGGAGAACATTGCG
 TAGACCGCCACCCAGGGTGCTTCCTTAGATCAATCCCGCGTGTAATTAAGCGTAGGGGAGACGCTCCTGAGAACAGACTCTCAGCTAAGCGTAGGAGGAGCATTTTTTTTGGATGAGGCCTCCTCTGTGGATACAAACGGCTCGGTCAACCAGCCACACGAATCAAGTGGAGGATATGTTGTAGTCCGCTCATTCCGAACTTTTAC
 GATATTTACGCAGTCGGACACCCCTCTTCCTTAATGCTTCGTTAAAATATCGGTCCGTGCGAGTTCTGGTGGCCCGTAGGCCTCGCTACTTAGAGGTGGGCCCCCAAGGGCACGCATAATCGGCGCCTACCGCGGTAGATCAAAGTGAACGAAGATCTTGTAAAGATTCTATGCGGAGGCAGAACATCTTACTAGGTAAGAGATTC
 GCTAAAGCTATCCAAGGATACCGGGCGGTGCTAAACTATTACAGTATAACATCAATCAATCACCGCTTCGCCTTCCTCGTAAGTCATACTGCATATGGGCTTCCACTATAGAGTAATCCCGTGAGTGGACGAGAAAGCACTACTAGACAACACGGACACCGTTACAGTCATAGTTGCGGCAGTGCTCATAAGTCCTTCACACAGGG
 TCCCGCTATATCTGATCTTTGTGACTGCTGGGGTATAACTCAGCTGGCACAGAACAGACCCGTAGTCCAGAAAGACTTGAGTATAATGACGCCATGCTCGACCGGAGGTCAAGTACGGGAGAGGCTTACGCAGAATCCCCCAAGAGGCTCGTTAACTGACCGCAATCGATTTCAATTCCCTCCGAGCTCACCGAGCGCTGGTATAG
 TTCCTGACTGCTTGAGCCAGCGCTATATTGCGCGCAAACCAGTCGCGTGACGTACCGTCATACCGAGTGATGTAAAGTTGATTATTGGGATCAGCTAATTCCTCGCGGTGTTAGTTCATCACTTTTGAGTCCGACAGACTACTAGTTCACTACTTCGAAGTTTGCTCTTACAAGCGAGGAACGGCCTGCCGAGTATACAGGGGCGT
 CAGGCCTCGCGATTAACCTTATGCGGCCTCTCAGAGCCCCGTCTAGCGAAGGTAATATGAGAACAGACTACAGAGACTACGCTCTGCCCCCTAAGGACTGGGAATTTATGGCCCTATATCGCCCTTATTCGCCATAACTTCTAAGATTTGCTATTACCATTCTGAGGCAGTTTAACTAAATGGCTATCCAACCTATGAGGACTGAA
 GATCCAGAACAACTTACTAGTCCGTAGGGCTGGACCTCTTCATGCCCGGGCGTCGGGCACATACGCGTATCAAAATGGGAGATGGCATTATCTACTTCTCCTGTGATTTTGAACGTAGTCACCCCACATCATACTTTTCACACCTCGTACTGGTGATTCCATTCTACCCAACGATACGTAATTGACCCCGCTTTTGATTGGAATTT
 CAAGAGTCGTACGAGCCCTCCGTCATCAATGCTTGCGATTAGAGTTCACGGTAGAATCCACCAGAGCAGAAGAGAACGCCAGTAGCGACCAGAAAGCCTTTAGAAAAGGCAGACTACTAGAATGTTGTGTGTAAGTGTACCAAACATTGATTCGGACGGTTGTCGTGTTCGAACCAGGTGATTTGGTGAGGTTTCAGCGCCTAGTG
 TTGTGATGATCTTCGTAAACATCCGGTGGGAGCCCCCCTCTCCTCGATGACTGTTTGACTATGATCCATTTACCTTGACTCGCAGGACGACAAGCCATTATTCATGCCGTGTGATAAGAACGCTCTACTAGGTTCTGTCCATGCCCAGCACAGATCAAGGGACCCGGCGGGCCCGGGTCAGAACTTTGGTCACCATTCGCAAATCA
 AGAGGCACCTGGCGCCAAAGGCATTTAATGAACATGGCGAACTGCCAGACGAGCATGGTAGAACAGAAGCCTAGGACCATCCCGACATAACAACCACTATTTATAATTGAACTATCTTGGCACACACGCTATTGGCGTTGCACTGAGACCGTTCATCGCCTTCACTGTGACCATTCGCCTATAGACATATAACTAACTTGGCTTCA
--- a/chapter2/for_real/rosalind_ba2g.txt
+++ b/chapter2/for_real/rosalind_ba2g.txt
@ -0,0 +1,21 @@
 15 20 2000
 AGTGGTTTAATCGGACGAGGCGTGTCCCTCAGCCCGATAACCATCCCGTCCTGTGTGCGACCGTTGAGCATCGTATTAGTTCCGTAGGATTTTGCGGTCGTCTATTTGATATAAAGTCAGGTATATATGGCCACAAGTTCGCGTGGACCGTTAGCGCACCAACACTGTAATATAACTGCCTTAAGGTAGCGACTCGCCAAGCGCAGGGGCAGCCCTGACAGTTTCCACGAAACTCAAGAGAGTATGTAGCGACAGTCCTTCGCAAGACAATCGTACGTGTCTACCGAAACTTAATTTCGTTAGTGGTTTAATCGGA
 CGAGGCGTGTCCCTCAGCCCGATAACCATCCCGTCCTGTGTGCGACCGTTGAGCATCGTATTAGTTCCGTAGGATTTTGCGGTCGTCTATTTGATATAAAGTCAGGTATATATGGCCACAAGTTCGCGTGGACCGTTAGCGCACCAACACTGTAATATAACTGCCTTAAGGTAGCGACTCGCCAAGCGCAGGGGCATCGAAGAGTGTGCATGCCCTGACAGTTTCCACGAAACTCAAGAGAGTATGTAGCGACAGTCCTTCGCAAGACAATCGTACGTGTCTACCGAAACTTAATTTCGTTAGTGGTTTAATCGGA
 TCGCTAAGTGGTGATACCGGCTGATAAGAAAGTAAGATTTCAGCATGACCCTGTTGATTCCACCCCTTCCTTTCATGGTGAGGCTTGTCTTTGCGGCGCCTCACGGTACCTGTGGACTGTACACACGAAGCACAACTTCCGAACTATTCGTTTGTAGACTATAAATCACCATGCTCATCAAGCTCAAAATTTCTCCTTACACCGACCGCGGTGGGAAAAAACGCAACGAAGCTCCAATTATCTCCAGTCTCTGCACGTGTAGAGATGGTGGAAAGCTAAGAGATGCCTTCGCCACATTAAGTCCCGCACAACGTTA
 ATTGGCAAAACCGATAGGATCCCGCGACTATGACGTCGCTTTTCGCTAAGTGTGGGCTGACCCTCCTACAAATAAGTCTCGTTTTAACCCTGGCCATTGCTTACAACCGCCGAAGTCGCGCTTCAATCAAAGGTGCAGGGTTATAATAGACATACAATTAGGATGTTTGACCGACATGCCTTGTTAACTTTAATTGACGTTACAGATTGATTATGCGATCTCTTTATGTTCTCAATTTAATATACCTCCGCTGGTTCCTATTGGGAGCCTTCAACACATAATAAATCCTTGTACCTCTGATTGAGTCTCTTTGCCT
 ATGTTCCTTAAGTAATTAATAGTACGTACACCGGTATTCGCTAGCCGTGCATCTTGACCCCCCCAAGGCGAACAGTTTGGATTTGCGAAGTCCCACGAAGGGGGCTTAAGGCTTGAGCCACATCCAGTTATGAAAGTATATCATCGGCACCCAGGAGGCTAGACAGGAGGTCAGAAAATTCCGCATTAGCGTCGTTGCGCAAGGCCGTCGCCGCCCGTGCTTCCAGGATTAGATCGCCTGCCAGACAGTCCGACTCCGTTGACAATAGAAGACAAGCTTATGCCCCGATTCACTCACCACCCAGACAGGCCCGCAT
 TGCTCGGACTGATATCCGCGTATGCGTACGTAATGTCTAGCAGGCGGTCGAGCCATAGGCTTCAATAGGGGTGTTGCGACTAAGCGATTGGCACAGGAAGCATTGGAATTAACACCGCAGTCATCTAAGTGTGCATACGGGCATGTGGAGATTTTTCTACGAATGATGCGTCAACGACCCATGGAATGAGTTTTTAGTTGTTACCCATTTTTATAATAACGTGCGCGGTTTATCTTATCCCTTATAATGATCTCTAACATAGGCGTACCTGAAAAGAATGCATTAAGCCGCAAAGGAGCCCAATTCTCAGCCGTCG
 AATCTAAGTTACTTCATGGTTCACGGTGCCACATCGACTGATCATCCATGCCTAGTGCTGTACTTAACCCATCATATTTCCTAAGTGCTTCGAACCCTTCGATCGGGGTGGTCATCTGTCCGTGACAAGGCTGCTAATAACCCACGCCGGTATAACACTGATTACGTTATACGCCTTATTCGGCAGTGACTGGCGTGCCACGTGCCAGGTAAAAAGAAATCTGGAACAGGGCTCCTCTTTCATAAGTGTGCATTTAAATAAGGGGAATAGTAAGGTCTCATTTGTAGTGCACGTGCCTTTCAATTATAGGCCCATA
 CGCCATCCACGTTTTAGTAATGTACCCAGGCCAACTAACACATAGCAACCGTCAGTTTTCACAGTTGTCATCTTGCCGCCCGAATAAGCCCCGCTGACCAACGTCTGAGGACGTTCTCCGCGGAGATGAGGGTATAGCGTCGTCGTACCTGCATTACCGAACAACTCTCCATCTTTAGGGAATTACCCATCTTAGCTATAGGACACAAGAGTCGACAGTAATTGTGGACTGGCTTTTGCGGTCTCGGTTCAATCAAGGAAAACCCTCTTGCACTACAATCGCAGCGTGTGCATTCAGAGCCCTTATCATACCTCGA
 AGGCGAGGTGAGGTCATGACCTGTCTAACCCCTTAGCGCCGGTGTAAATTCAATGCACGTAACGCTAGAGGCCTTAGGCCTCGATTCATCCTTGTGATCCATGTAATCGAACGACGCCTATCTAGTTCCGGAGCTTCGAACGAGGCCGATTAAAAACCCGTTGGCCGGTTGATCTGTGCTGCTCAAGATGTAACATCCCGAACTCAGCGCATCACGCCCCGCCAGAGCCTTTGGGAGCAGGGCCAGCGCTCGCTGGTTGTGCATGCGCTGCAATTCAAACACCTGTGGCACGAGTGCCCCAAAGGACCATCATCGA
 TTGCAATACAGTGCCCCTTGTGCTGTTTGCTAGGCGAATACAGGCGACCGACACAAAGCCCGGCCCTATATCAGTACGAGGCAACATACTGCTCGCTAAACTAGCGTATAAATTTGGACACCATAATGCGCAATGCACGCGGTATAGGTGGTCTTGTGGTAAGAGGGATTTCTAAATATCGTATTCCCCAACGCAGGTATACGAAGCCCATGGTAATTTAAGCGTTTAAACAGCTAGAACTCGCTCGCTCTTTGTGCATGTACTAGGTCCTTGTGTAGAAGAGGCGCAATGCCTTGCTATAGACCTTTGTCCCGTC
 GTGCGAAAATGCATAATTATAACTTTTCGCCTCGGGCGCGTCCACGGTATTACGAAGTCGAAGCGCGCATCCACTGACAATTCACAGACAGCAAAAATTGTTGCATTTAATCACGGGGACCCTATGGTGCAGTTGCGAGACCACATATGACCGGCTTTGTAGCACCGGCCCCAGTTTAATTCCCCTGACTAATGGTAGATACGACGACCGCCCCCCACAGACTCACTCACCTCCAGCACCAGCTCAACGGTGACCCCTTTCTGTTCTAATGCGGTATTCGCTAAGTGTCACTAAGGTTAGTGCGGCTTTTGCTGCA
 GTAGTCCGTGGCATATGGAAGGGGAGCTTTACTCCCTGATCGGTGAGTGTGGAGACGTTTAGCGTACTGGTCACGGCAAGAGACGTTGTGAGTGTTGTATATGTTTCTTAGGAAAGCGGACGGCGTTACGCATGAGTAAGACGGCCTAAAGAATGAACCATGATTGATAATCTATTAATTGTTAGGTAAGGATAAGCAAAAAGGTGCTGCTGGGTCTTCAAGTAAGGGATATTCCCTCGCAGTGTGTGCATGACTCATATGGTTAACCCGTCTAAGCAAAAATCTCGACAGGAAGGTGAGTCGGCGCCATATGAGG
 GGCGACAGCTGGTAACACGGCTATCGGGGCCGAATTGCCGACACTTGGCGCATCGCTGGAAGTGCTTCAGATAGTTATGACGGTGAAACACGCTCCGGCACAGCCTATAGTATGTTCGTAGCGTACAAAAGCTAGGCAGCCGTAATATCAGCGCTTAATGCTTTAATTGGCATGTGTCCTATTTGTGACGTTGATGTCGATGATAATCCGCACAGAACAACTCATGCATATTCGACGAGTGTGCATGATAGACACTGCGTTGTTGCCATGTATCTCCTGAAGCACGCACACAACGAAGGTCGCGTGCTTTTTCCGG
 ATACTACGATCAAGCGAAAAGGGGACAATCGTTGGCAGGGTCACTAGGGCAGGGTCTTAGAGAATCAGTGCAACGTTTTAATTCGCTCACCTGTGCCGCTAAGTGTGCGATGTGTAATCTCCAATGGGAAATGAATCCTTCGGCTCGAGTAATGATTGCGTATGGTATTGGCCCAACGTAGGACTCAAGTCCCTGGTCGTAGCGCGATCTGTAATGTAAACTTACCATACGAGCAGGCTACGTTGAGGAGCGCTCGCGGAACGGTATAGAAAACGGTACGTCATATTGGCCCTTGTGACTCCTCCTCCGCTTGGAT
 TTTTATTACATCTGTTCGCTAATCCTGCATGGTAAACAGTTACAGGAATTGCGATACTCCACTGGGCCACCACTACTTCACTAACTGGTAAAATGCCGGTCAGCTCATAGGTCCAAATAACGTTTATGGGTGTTAGCAATGTTAGCGATGCGATCTGTAAGATCCGAATCGTATCACAGCGCGCTCCTGCCAACGTCACCTGCTCCACCTAGCACTTGTCGATAACTCCCCCTCCAATCTACAAACACCAACTCGAAAATTGACACGCGCTTCTCGGCTGTTGGTGCACTCTGATGTTAATATGATGCCATGAGCC
 TGCCAGATACCTACCCTCTATATTCCAAACGTGAGTGAACTAAGTTCGATTACGAACCCGTACGTGGCTGAGCACGGCTAGTACCGGCCCGATTGTACCGTTCATATTGATTAGAGTGACCGGAGCACACAATCATCGCCCCCTTAAGCTATAACTGTCCCCGGAGCCTGAGCCTTTGACAACTTCGATAGGTTAATAAAAGAGTCTCGCTAAGTAGCCATATGATGAGTGATAGGGAGGCCTAGACCTGGACAACCCCTCATTTACGTCCGAACTCGGAGTGAAGTGTAATGTGAGCTCTTAAAAGGAGCTGGAT
 AGGCTCTCTGATTTAGCGGTGACCGCGTCCCGATTCTCACTCCTCAGAAGGTCTGGTAGCGCTACGGGGATGGGAACCCAGACACTCGAATCGAATCGGTATGACACTAGTACAAGGGGGCCTTTAACGCACGAGAATAACACAATTCCTTCGCATACATAGCTAACAGCAGACATAGGTCTTGATAAAAACTGTGCTGCTTCCTCAGAGTCGCTAAGAAAGCATGCCAGTGCACACTGGACATTACGCCGCAGTACAGCAATTCGCGTCTCAGATCAACCTGGGGAAATAAAACGTCTTTGCGTTAGCCCTTTGT
 TGCCTTGATGTCCAGGCATAGGTCATGTACGGGCTACCGTCATGTCCATGTCAGAATCCGAATGATCCTCTGGATTCCGATCCCGGCAGAGGGTAACTGTGCGACCTCAGCTTCCTCATCCCGCTATCGCTCACGGCCGGTCCTAGTGCGGCATGGATAAGCTCATCCAGGATGATTTACCCAAACCCTTTCACGTGGTGGTGGGGCGCGACTGTCACGCAGGAGAGTCGCCCGAGCTGTGGGCAGGAATACTTTCCTAAAGTGTGCATGTTAGGAAGAGACGTTAACTGCGCCTCCCTATCCTATCTGAGTGGCG
 ATAACGACCTGTGTGTTCATCGTATCTTCTCGAACACTTATGTAGATTCGCGTGGCTACGTTGTACATTCACTCCACTCAAGAGCGAAGGGTGACGTTTTCACTCCTCGCTGGAAAACCTAGAACGGGCTGTTTTTTACGATCAAAACAAAACCACTTGATAATTGTACTATTGTCTGGTAAGCTAAGTGTGCAATCAAGATCAACTCAATCCCCTGCCACCATAGTGTGGGCACCACGTAGAGAATTCGTCGAACAGATAACGCAAACTGACAGGGAGCTTAATGAACCATCAGCCGATCACCTTCGTGAGCATC
 TCGCTACTGGTGCATCCTATCTATTGATATTGACAACCCGGGATTAGTGACAACCGATTTCAGACTAAACTAGTTAGTAAAGCATTTCTCTATCTCCGCCGAGTGGACGGTGATCTAAGCAAGTAGGTGCCAGGAGGCCCATAACCGCCAATGACTTTCATGATCTAATCGACGGTTCGTTTTGAGGTTGGGGTACGCTCATAACCTTTATGTTTTGGTACACGCCTGTCACCTGCGCCGTGGTATCTGAGACATTTGTCTCCTGGACTAGTTGATTCCAGTATTCACAGAACGCCGGGATACGTTTCCGTCAATA
--- a/chapter2/populate_templates.py
+++ b/chapter2/populate_templates.py
@ -0,0 +1,77 @@
 import jinja2
 import os
 def main():
    # Jinja env
    env = jinja2.Environment(loader=jinja2.FileSystemLoader('.'))
    problems = [
        {
            'chapter': '2',
            'problem': 'a',
            'title': 'Implement Motif Enumeration',
            'description': 'Given a collection of strings of DNA, find all motifs (kmers of length k and Hamming distance d from all DNA strings).',
            'url': 'http://rosalind.info/problems/ba2a/'
        },
        {
            'chapter': '2',
            'problem': 'b',
            'title': 'Find a Median String',
            'description': 'Given a kmer length k and a set of strings of DNA, find the kmer(s) that minimize the L1 norm of the distance from it to all other DNA strings.',
            'url': 'http://rosalind.info/problems/ba2b/'
        },
        {
            'chapter': '2',
            'problem': 'c',
            'title': 'Find a Profile-most Probable k-mer in a String',
            'description': 'Given a profile matrix, find the most probable k-mer to generate the given DNA string.',
            'url': 'http://rosalind.info/problems/ba2c/'
        },
        {
            'chapter': '2',
            'problem': 'd',
            'title': 'Implement GreedyMotifSearch',
            'description': 'Find a collection of motif strings using a greedy motif search. Return first-occurring profile-most probable kmer.',
            'url': 'http://rosalind.info/problems/ba2d/'
        },
        {
            'chapter': '2',
            'problem': 'e',
            'title': 'Implement GreedyMotifSearch with Pseudocounts',
            'description': 'Re-implement problem BA2d (greedy motif search) using pseudocounts, which avoid setting probabilities to an absolute value of zero.',
            'url': 'http://rosalind.info/problems/ba2e/'
        },
        {
            'chapter': '2',
            'problem': 'f',
            'title': 'Implement RandomizedMotifSearch with Pseudocounts',
            'description': 'Re-implement problem BA2e (greedy motif search with pseudocounts) but use a random, instead of greedy, algorithm to pick motif kmers from each DNA string.',
            'url': 'http://rosalind.info/problems/ba2f/'
        },
        {
            'chapter': '2',
            'problem': 'g',
            'title': 'Implement GibbsSampler',
            'description': 'Generate probabilities of each kmer in a DNA string using its profile. Use these to assemble a list of probabilities. GibbsSampler uses this random number generator to generate a random k-mer.',
            'url': 'http://rosalind.info/problems/ba2g/'
        },
    ]
    print("Writing problem boilerplate code")
    t = 'template.go.j2'
    for problem in problems:
        contents = env.get_template(t).render(**problem)
        fname = 'ba'+problem['chapter']+problem['problem']+'.go'
        if not os.path.exists(fname):
            print("Writing to file %s..."%(fname))
            with open(fname,'w') as f:
                f.write(contents)
        else:
            print("File %s already exists, skipping..."%(fname))
    print("Done")
 if __name__=="__main__":
    main()
--- a/chapter2/template.go.j2
+++ b/chapter2/template.go.j2
@ -0,0 +1,49 @@
 package rosalindchapter{{chapter}}
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA{{chapter}}{{problem}}: {{title}}
 func BA{{chapter}}{{problem}}Description() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA{{chapter}}{{problem}}:",
 		"{{title}}",
 		"",
 		"{{description}}",
 		"",
 		"URL: {{url}}",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA{{chapter}}{{problem}}(filename string) {
 	BA{{chapter}}{{problem}}Description()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	//// Input file contents
 	//input := lines[0]
 	//params := lines[1]
 	//result := rosa.PatternCount(input, pattern)
 	// 
 	//fmt.Println("")
 	//fmt.Printf("Computed result from input file: %s\n", filename)
 	//fmt.Println(result)
 }
--- a/chapter3/ba3a.go
+++ b/chapter3/ba3a.go
@ -0,0 +1,60 @@
 package rosalindchapter3
 import (
 	"fmt"
 	"log"
 	"strconv"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA3a: Generate k-mer Composition of a String
 func BA3aDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA3a:",
 		"Generate k-mer Composition of a String",
 		"",
 		"Given an input string, generate a list of all kmers that are in the input string.",
 		"",
 		"URL: http://rosalind.info/problems/ba3a/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA3a(filename string) {
 	BA3aDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Input file contents
 	k_str := lines[0]
 	k, err := strconv.Atoi(k_str)
 	if err != nil {
 		msg := fmt.Sprintf("Error: string to int conversion failed for %s\n",
 			k_str)
 		log.Fatalf(msg)
 	}
 	input := lines[1]
 	result, _ := rosa.KmerComposition(input, k)
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	for _, kmer := range result {
 		fmt.Printf("%s\n", kmer)
 	}
 	fmt.Printf("\n")
 }
--- a/chapter3/ba3b.go
+++ b/chapter3/ba3b.go
@ -0,0 +1,54 @@
 package rosalindchapter3
 import (
 	"fmt"
 	"log"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA3b: Reconstruct string from genome path
 func BA3bDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA3b:",
 		"Reconstruct string from genome path",
 		"",
 		"Reconstruct a string from its genome path, i.e., sequential fragments of overlapping DNA.",
 		"",
 		"URL: http://rosalind.info/problems/ba3b/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA3b(filename string) {
 	BA3bDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Trim each line and there are your contigs
 	for i, line := range lines {
 		lines[i] = strings.Trim(line, " ")
 	}
 	genome, err := rosa.ReconstructGenomeFromPath(lines)
 	if err != nil {
 		log.Fatalf("Error when calling ReconstructGenomeFromPath()")
 	}
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(genome)
 }
--- a/chapter3/ba3c.go
+++ b/chapter3/ba3c.go
@ -0,0 +1,54 @@
 package rosalindchapter3
 import (
 	"fmt"
 	"log"
 	"strings"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA3c: Construct the overlap graph of a set of k-mers
 func BA3cDescription() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA3c:",
 		"Construct the overlap graph of a set of k-mers",
 		"",
 		"Given a set of overlapping k-mers, construct the overlap graph and print a sorted adjacency matrix",
 		"",
 		"URL: http://rosalind.info/problems/ba3c/",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA3c(filename string) {
 	BA3cDescription()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	// Trim each line and there are your contigs
 	for i, line := range lines {
 		lines[i] = strings.Trim(line, " ")
 	}
 	g, err := rosa.OverlapGraph(lines)
 	if err != nil {
 		log.Fatalf("Error when calling ReconstructGenomeFromPath()")
 	}
 	fmt.Println("")
 	fmt.Printf("Computed result from input file: %s\n", filename)
 	fmt.Println(g.String())
 }
--- a/chapter3/chapter3_test.go
+++ b/chapter3/chapter3_test.go
@ -0,0 +1,9 @@
 package rosalindchapter3
 import "testing"
 func TestChapter03(t *testing.T) {
 	BA3a("for_real/rosalind_ba3a.txt")
 	BA3b("for_real/rosalind_ba3b.txt")
 	BA3c("for_real/rosalind_ba3c.txt")
 }
--- a/chapter3/for_real/rosalind_ba3a.txt
+++ b/chapter3/for_real/rosalind_ba3a.txt
@ -0,0 +1,2 @@
 50
 GGGGGAAACTTACGGAGTACAAGAAGACCCGGCACAAAGAGAAAACACGTTGCTCGTTAGCTTAAGTTAAGACGTATCGGATATCTATCGTATCCTCGTAGTATTGCTAGCCACTTCACTGGACCAGGCTTACGTATTAGCCTTATGACCCCATTTCGTCTCCGCTGCTACAGCTGTGGAGTTGACGCGTCCGGTGGGCCCTCCGTTAGCAGGTCAGCTCATATTTTCGGCAAGAAATTACCCGGAACGGACCGAAAATGGGGTACAACATGCCCACCCACAACTTAGTACACAACGCTCAGCAAGTAGCTAACGACCGCTGCCGTCGTCAGTATTAGACGCACTTAACCGTACGGAATCCGTGAGTCCTGTTTCCGCCGATCGAATTACGCGCCCGGGTCGTGGGTCCAAAGGTGGCCGATCTCACGTACTGGTGAGTCGCGCGGTCACTTGGCTGTGAGGTCCACCGGCGGCCACAGTAATCTCTGGTGCACCCAGAATCGAGTCTGGATTGTGCACAAAGCTGCCCGCCTCTATTTCTCGGACCTGGCAGAACGCAACGGATGGGTTGAAGATTGGGCCGGTTCCGATGCCCCAAAGTACCCACATTTACTAGGGTGAGGCTGTTCTTTTGAGAGTAGAGACGAAAGCACCCCGACGTAACTGCTGCACACGGGGCTGCTCGGGATACTGTGCCGGAACTAGCGAGGCTCTACCCTCATCGGAAACCAGGCCTCATAATTCTTACAGCGTACTGTGTACTCCACAAGGAGCTGACCAGACATTCCACGTCCATGGATTCGGCTCATGCATACCTCCCGATCCACTCCTGAGCACATTGGATGGACACTTGAACGATGTCCTTAGCGCACGAGACATCAATTCGTGACGGTAGATTGCTCTCACCCTGATGCGGGTAAGTCACGTATTACCCGGCGTGCGGTATGTAGTAATACAGCTATCTACAACAAATGCAACCCGGCAGGTCTCCCATAGACCA
--- a/chapter3/for_real/rosalind_ba3b.txt
+++ b/chapter3/for_real/rosalind_ba3b.txt
--- a/chapter3/for_real/rosalind_ba3c.txt
+++ b/chapter3/for_real/rosalind_ba3c.txt
@ -0,0 +1,981 @@
 TGTACCTCGGGCTTTAAGGT
 CGGAACGGGAATCCTGGGAG
 ACTAGCTGCACTATCGGTTT
 CGATCTCCAGGAAGATGTTG
 AGCGGGAACTGCTGCAGGGC
 GGGCTCCCGCGCCAGTGCCC
 AATGCCTTTCTTTAGGCAGC
 AGAAACCGAAATCGTGCCCC
 TCATGGTTACAAAATTTACG
 CCAGGTCAAAGGGAGCTATA
 GCGCCCTGGTAAGTTACGCA
 GACAATGGCCCGTGTGAATG
 CGACTAGATAGATCCAATTG
 ATTTTGGACCGCTGTCCTTC
 CGACGTTCAGCGAAGAACGA
 ACAGCCATCAAAGGAGAGCC
 AGCAACAATAATTACGTCAC
 AAATGGTCGAAACTAGCTGC
 CAACCTGAATGTCGGGTCCG
 AAAATTTTGGACCGCTGTCC
 TGGTATCTCAAGAACCCTCT
 GGAGGGCCAACCTGAATGTC
 ACTTGTAACCCGTCGGAACG
 GCCATTTGTGCCTTTTTGGT
 GAACCCTCTCTCTACAGGCT
 GTGCCTTTTTGGTGTGGAAC
 AAGGTCCCACACAGCGTGCC
 TCTCTCTACAGGCTAGTCAT
 CTGCTGGAAACGACTAGATA
 GCTTTAAGGTTAGGGGGTAA
 AGCGAGGCCCTTGACACGAA
 GATTGAATAGAGATATTCGA
 CTCTCTCTACAGGCTAGTCA
 CATCTTTTTGCCCATTATAA
 CTGCAGGGCTCCCGCGCCAG
 CATTAACACGACGTTCAGCG
 TTCAGCGCCCTGGTAAGTTA
 GAATGTGGAAATCGATCGTA
 ATTCAGCGCCCTGGTAAGTT
 TTTGGCCGAACCAGGTCAAA
 ATCGGAGGAGTAGTTGGTAC
 CGAAATCGTGCCCCATGTTC
 GGTTGTGATCAGCGGCCGGG
 GCAGCATTCAGCGCCCTGGT
 GAGGTCCATTATTAACACGG
 CCCATTATAATCCACATGGC
 GTGATCAGCGGCCGGGACAA
 GGGCCAACCTGAATGTCGGG
 CGGAGGAGTAGTTGGTACCA
 GCGAAGAACGAATACGACAG
 GTCACCATTCCCAGCAAATG
 CAACTTGTAACCCGTCGGAA
 CCCGTGTGAATGTGGAAATC
 ACAGAGCGAGGCCCTTGACA
 TGTCCTTCCAGTGCTCGCGG
 GCAATTACGAATGACCAGGC
 AGAACGAATACGACAGAGCG
 CTAGTCATGCGGGCTCGCAC
 ATCCAGGAGAGATTGAATAG
 GAGAGTCACATACACAATGC
 TCCCCTGGAAGCGCGCTCCC
 GTTGGTACCAACGCAAGAGG
 AAATCGATCGTATACCGCAG
 CAGCCATCAAAGGAGAGCCC
 GTCCATTATTAACACGGGCT
 TTAGGCAGCATTCAGCGCCC
 GATCAGCGGCCGGGACAATG
 ATTACGAATGACCAGGCTCA
 GAGCCCCTTGCGCTGTATCG
 TGGTCACTTGCTGCTGGAAA
 AAAATTTACGTCCGAGCTAT
 GGAGTAGTTGGTACCAACGC
 GAAACGACTAGATAGATCCA
 GTGCATCCAGGAGAGATTGA
 GCCGAAATCACGCGCATTGT
 TAGCAACAATAATTACGTCA
 CTCAAGAACCCTCTCTCTAC
 GAATCCTGGGAGGGCCAACC
 TGCCCCATGTTCGCGTTTAA
 CAATGCGGCTGTCGATCTCC
 GGGAGCTATAACAGCCATCA
 TACGAATGACCAGGCTCAAT
 GACATCAAGGTCCCACACAG
 CCTTCCAGTGCTCGCGGGGT
 TTTCTTTAGGCAGCATTCAG
 TCCCAGCAAATGCCTTTCTT
 ACTGCTGCAGGGCTCCCGCG
 CGTTCAGCGAAGAACGAATA
 GGAACGGGAATCCTGGGAGG
 GGCTAGTCATGCGGGCTCGC
 GGTCGAAACTAGCTGCACTA
 TCGGCAAAGTTAGAGCGGGA
 CAGGTCAAAGGGAGCTATAA
 ATAGCAACAATAATTACGTC
 TAATTACGTCACCATTCCCA
 GCAAAAATTTTGGACCGCTG
 GGTCAAAGGGAGCTATAACA
 TAGCTTCACAAATGGTCGAA
 GGAACTGCTGCAGGGCTCCC
 CACTTGCTGCTGGAAACGAC
 CCTGAATGTCGGGTCCGAGT
 AGGTTAGGGGGTAAGGCCAT
 CCAGCAAATGCCTTTCTTTA
 GGAGAGCCCCTTGCGCTGTA
 CCCATTCTTCCCCTGGAAGC
 CCATTCCCAGCAAATGCCTT
 TCGAGAGTCACATACACAAT
 AACCCTCTCTCTACAGGCTA
 CATGTTCGCGTTTAAGATGA
 GATCCAATTGGCCGAAATCA
 GTAGTTGGTACCAACGCAAG
 AACGGGAATCCTGGGAGGGC
 TGGAAATCGATCGTATACCG
 ACCGCTGTCCTTCCAGTGCT
 CGAGCTATAGCAGCAAAAAT
 AGCCCCTTGCGCTGTATCGT
 GATATTCGAGAGTCACATAC
 CGAGTTTGGCCGAACCAGGT
 ACCAGGTCAAAGGGAGCTAT
 CAAAGGTGGTTGTGATCAGC
 TCAGCGGCCGGGACAATGGC
 GGTAAGGCCATTTGTGCCTT
 GAAGTTCGGCAAAGTTAGAG
 AAAAATGGTATCTCAAGAAC
 AAACGACTAGATAGATCCAA
 ATCGTAGCTTCACAAATGGT
 TGAGTGACATCAAGGTCCCA
 CATTCTTCCCCTGGAAGCGC
 GGTCCCACACAGCGTGCCAT
 CAATTACGAATGACCAGGCT
 CTTGTAACCCGTCGGAACGG
 TGATCAGCGGCCGGGACAAT
 ATCCACATGGCTATAGCAAC
 GGCTGTCGATCTCCAGGAAG
 CACATGGCTATAGCAACAAT
 TTAAGATGAGTGACATCAAG
 GAGATTGAATAGAGATATTC
 CCTGGGAGGGCCAACCTGAA
 GGGCTTTAAGGTTAGGGGGT
 AGAGCGAGGCCCTTGACACG
 CCCACACAGCGTGCCATTCA
 TGGCTATAGCAACAATAATT
 CCTGGTAAGTTACGCATTAA
 GCCCTGGTAAGTTACGCATT
 CCCGTCGGAACGGGAATCCT
 ACGTTCAGCGAAGAACGAAT
 AAGTTACGCATTAACACGAC
 GCATCCAGGAGAGATTGAAT
 GGTTTGGTCACTTGCTGCTG
 CCCGCGCCAGTGCCCATCTC
 CCGCTGTCCTTCCAGTGCTC
 GTGTACCTCGGGCTTTAAGG
 ACAAAGGTGGTTGTGATCAG
 CAGTGCTCGCGGGGTGTACC
 AATCGTGCCCCATGTTCGCG
 CCTTTATCTCGTGCATCCAG
 GGGAACTGCTGCAGGGCTCC
 GAAATCGTGCCCCATGTTCG
 TAACACGGGCTCATCTTTTT
 AACACTAAACAAAGGTGGTT
 ATGTTCGCGTTTAAGATGAG
 GCTGCTGGAAACGACTAGAT
 GTATCTCAAGAACCCTCTCT
 CCAACGCAAGAGGTCCATTA
 CACGGGCTCATCTTTTTGCC
 TGCTGCTGGAAACGACTAGA
 TTGTTGTCGTCATGGTTACA
 CGCACGCGGTCAACTTGTAA
 GCCGGGACAATGGCCCGTGT
 GGAATCCTGGGAGGGCCAAC
 TAGATAGATCCAATTGGCCG
 AATGGCCCGTGTGAATGTGG
 CTTCACAAATGGTCGAAACT
 AGAGCGGGAACTGCTGCAGG
 TCCAGTGCTCGCGGGGTGTA
 ACACAGCGTGCCATTCATCC
 TCTTTAGGCAGCATTCAGCG
 CCAGTGCCCATCTCGGCGAA
 TACAGGCTAGTCATGCGGGC
 GTCGGAACGGGAATCCTGGG
 TCGGAACGGGAATCCTGGGA
 GAGTAGTTGGTACCAACGCA
 CCCTGGAAGCGCGCTCCCGC
 AACAATAATTACGTCACCAT
 CTGAATGTCGGGTCCGAGTT
 CGCGTTTAAGATGAGTGACA
 TCGGGCTTTAAGGTTAGGGG
 ATACCGCAGAAGTTCGGCAA
 ACGAATACGACAGAGCGAGG
 TGGTTACAAAATTTACGTCC
 CGCATTAACACGACGTTCAG
 GCGAAGAAACCGAAATCGTG
 ACTAAACAAAGGTGGTTGTG
 TTGCCCATTATAATCCACAT
 CCGGGACAATGGCCCGTGTG
 TCCAGGAGAGATTGAATAGA
 TAATCCACATGGCTATAGCA
 AATGGTCGAAACTAGCTGCA
 AAGAACGAATACGACAGAGC
 AATCCTGGGAGGGCCAACCT
 CGAAGAACGAATACGACAGA
 AATGCGGCTGTCGATCTCCA
 AGATGAGTGACATCAAGGTC
 ATCTCAAGAACCCTCTCTCT
 GTGCCCATCTCGGCGAAAAA
 ATAGATCCAATTGGCCGAAA
 AGGCCCTTGACACGAACACT
 CACAAATGGTCGAAACTAGC
 ATTGTTGTCGTCATGGTTAC
 TGTCGATCTCCAGGAAGATG
 GTTCGGCAAAGTTAGAGCGG
 GTCAAAGGGAGCTATAACAG
 CACGACGTTCAGCGAAGAAC
 CGTGCCCCATGTTCGCGTTT
 TGGACCGCTGTCCTTCCAGT
 TCTCGTGCATCCAGGAGAGA
 AGTGACATCAAGGTCCCACA
 CTCTACAGGCTAGTCATGCG
 CAGCGGCCGGGACAATGGCC
 CGTCCGAGCTATAGCAGCAA
 GCGGCCGGGACAATGGCCCG
 GAAGAAACCGAAATCGTGCC
 AGGAGAGCCCCTTGCGCTGT
 CAAGGTCCCACACAGCGTGC
 GTGCTCGCGGGGTGTACCTC
 CTTCCCCTGGAAGCGCGCTC
 GGCTCAATCGGAGGAGTAGT
 GAACCCATTCTTCCCCTGGA
 GTATACCGCAGAAGTTCGGC
 GAATGACCAGGCTCAATCGG
 ATAACAGCCATCAAAGGAGA
 GAGCTATAACAGCCATCAAA
 GGTCCGAGTTTGGCCGAACC
 CCCCTTGCGCTGTATCGTAG
 CTGGTAAGTTACGCATTAAC
 CCTTGACACGAACACTAAAC
 AGATCCAATTGGCCGAAATC
 AGTGCTCGCGGGGTGTACCT
 GTCAACTTGTAACCCGTCGG
 TACGCATTAACACGACGTTC
 ACAAAATTTACGTCCGAGCT
 GCAACAATAATTACGTCACC
 CAATTGGCCGAAATCACGCG
 ACCCGTCGGAACGGGAATCC
 GGTTACAAAATTTACGTCCG
 ACGACAGAGCGAGGCCCTTG
 ATTGAATAGAGATATTCGAG
 TCATGCGGGCTCGCACGCGG
 GCAAAGTTAGAGCGGGAACT
 TGTATCGTAGCTTCACAAAT
 CCCTCTCTCTACAGGCTAGT
 TCTACAGGCTAGTCATGCGG
 GATAGATCCAATTGGCCGAA
 CCGAAATCGTGCCCCATGTT
 TTTAAGGTTAGGGGGTAAGG
 CCGCCTTTATCTCGTGCATC
 GGCCGGGACAATGGCCCGTG
 AATGTGGAAATCGATCGTAT
 ACACGGGCTCATCTTTTTGC
 GAATGTCGGGTCCGAGTTTG
 TGGAAGCGCGCTCCCGCCTT
 GCTCCCGCCTTTATCTCGTG
 CGCCCTGGTAAGTTACGCAT
 GTCGTCATGGTTACAAAATT
 GCGGTCAACTTGTAACCCGT
 ATCGTGCCCCATGTTCGCGT
 GAAACCGAAATCGTGCCCCA
 TGTGGTGCAATTACGAATGA
 CGAAATCACGCGCATTGTTG
 AACCTGAATGTCGGGTCCGA
 CGCCTTTATCTCGTGCATCC
 GTTTAAGATGAGTGACATCA
 ATAATTACGTCACCATTCCC
 AGGAGTAGTTGGTACCAACG
 GGTTAGGGGGTAAGGCCATT
 TCATCTTTTTGCCCATTATA
 ACAAATGGTCGAAACTAGCT
 TCGCGGGGTGTACCTCGGGC
 CGGGCTCATCTTTTTGCCCA
 GCCATCAAAGGAGAGCCCCT
 TTTACGTCCGAGCTATAGCA
 TGCGCTGTATCGTAGCTTCA
 ACGACTAGATAGATCCAATT
 ACAATGCGGCTGTCGATCTC
 GTGAATGTGGAAATCGATCG
 CCGAAATCACGCGCATTGTT
 TGGTGCGAAGAAACCGAAAT
 CTATCGGTTTGGTCACTTGC
 CCCAGCAAATGCCTTTCTTT
 ACCCTCTCTCTACAGGCTAG
 GCTGCAGGGCTCCCGCGCCA
 TGCGGCTGTCGATCTCCAGG
 CCAGGCTCAATCGGAGGAGT
 TTCGAGAGTCACATACACAA
 AATTACGTCACCATTCCCAG
 GGTAAGTTACGCATTAACAC
 CTGTGGTGCAATTACGAATG
 TGTTGGTGCGAAGAAACCGA
 AGGGCCAACCTGAATGTCGG
 AAGGTTAGGGGGTAAGGCCA
 AATTTACGTCCGAGCTATAG
 ATACACAATGCGGCTGTCGA
 TCGTGCCCCATGTTCGCGTT
 CAGAAGTTCGGCAAAGTTAG
 TTGAATAGAGATATTCGAGA
 TCAGCGCCCTGGTAAGTTAC
 AAATCGTGCCCCATGTTCGC
 ATGCCTTTCTTTAGGCAGCA
 TGTCGTCATGGTTACAAAAT
 CCATGTTCGCGTTTAAGATG
 GCATTCAGCGCCCTGGTAAG
 CCCATGTTCGCGTTTAAGAT
 ATCCTGGGAGGGCCAACCTG
 AACACGACGTTCAGCGAAGA
 GAATAGAGATATTCGAGAGT
 GTACCTCGGGCTTTAAGGTT
 CAGGCTCAATCGGAGGAGTA
 TTTAGGCAGCATTCAGCGCC
 ATTCTTCCCCTGGAAGCGCG
 ACGAATGACCAGGCTCAATC
 GGCTCATCTTTTTGCCCATT
 GAGCGAGGCCCTTGACACGA
 AATGACCAGGCTCAATCGGA
 AAGAGGTCCATTATTAACAC
 GGGTGTACCTCGGGCTTTAA
 TTTTTGGTGTGGAACCCATT
 TGACCAGGCTCAATCGGAGG
 ACACTAAACAAAGGTGGTTG
 GGGGTGTACCTCGGGCTTTA
 ACGTCACCATTCCCAGCAAA
 CGAAACTAGCTGCACTATCG
 CCTCGGGCTTTAAGGTTAGG
 TTAACACGGGCTCATCTTTT
 AAATGGTATCTCAAGAACCC
 TGACATCAAGGTCCCACACA
 GAGGCCCTTGACACGAACAC
 CTTGCGCTGTATCGTAGCTT
 GTCCGAGTTTGGCCGAACCA
 GGAGGAGTAGTTGGTACCAA
 TTCCAGTGCTCGCGGGGTGT
 GAACGAATACGACAGAGCGA
 CGGGTCCGAGTTTGGCCGAA
 AATTACGAATGACCAGGCTC
 GTCGGGTCCGAGTTTGGCCG
 TATAGCAGCAAAAATTTTGG
 AGTAGTTGGTACCAACGCAA
 TGCTGGAAACGACTAGATAG
 TGGCCCGTGTGAATGTGGAA
 TGTTCGCGTTTAAGATGAGT
 AGCGGCCGGGACAATGGCCC
 ATTCCCAGCAAATGCCTTTC
 TACCTCGGGCTTTAAGGTTA
 AGTCATGCGGGCTCGCACGC
 GGCAGCATTCAGCGCCCTGG
 CGAGAGTCACATACACAATG
 GTGTGGAACCCATTCTTCCC
 CATCCAGGAGAGATTGAATA
 GGCCGAAATCACGCGCATTG
 TTGACACGAACACTAAACAA
 TCTCAAGAACCCTCTCTCTA
 TGCATCCAGGAGAGATTGAA
 ATCTCCAGGAAGATGTTGGT
 CACATACACAATGCGGCTGT
 TTGGTGCGAAGAAACCGAAA
 AGTGCCCATCTCGGCGAAAA
 GCGCTCCCGCCTTTATCTCG
 TAGATCCAATTGGCCGAAAT
 GGCCCTTGACACGAACACTA
 CAAAAATTTTGGACCGCTGT
 CATCAAGGTCCCACACAGCG
 CAGCAAATGCCTTTCTTTAG
 CATACACAATGCGGCTGTCG
 ATCGTATACCGCAGAAGTTC
 GAATACGACAGAGCGAGGCC
 TCAACTTGTAACCCGTCGGA
 TGTAACCCGTCGGAACGGGA
 TGCAATTACGAATGACCAGG
 TCGTAGCTTCACAAATGGTC
 TCCATTATTAACACGGGCTC
 TTGGCCGAAATCACGCGCAT
 CCTCTCTCTACAGGCTAGTC
 ATTGGCCGAAATCACGCGCA
 GCTAGTCATGCGGGCTCGCA
 AGGTCCCACACAGCGTGCCA
 GGAAATCGATCGTATACCGC
 CGCGCCAGTGCCCATCTCGG
 TCGATCGTATACCGCAGAAG
 CCAATTGGCCGAAATCACGC
 ATACGACAGAGCGAGGCCCT
 CGCTCCCGCCTTTATCTCGT
 TGGCCGAAATCACGCGCATT
 AATAATTACGTCACCATTCC
 CAGCGAAGAACGAATACGAC
 TACGACAGAGCGAGGCCCTT
 GAAGCGCGCTCCCGCCTTTA
 TCTTCCCCTGGAAGCGCGCT
 GAGTGACATCAAGGTCCCAC
 GCGGGCTCGCACGCGGTCAA
 CGGCTGTCGATCTCCAGGAA
 CCGTCGGAACGGGAATCCTG
 GTAAGTTACGCATTAACACG
 ATCTTTTTGCCCATTATAAT
 AATACGACAGAGCGAGGCCC
 GACACGAACACTAAACAAAG
 GTGTGAATGTGGAAATCGAT
 TGCACTATCGGTTTGGTCAC
 GTCATGCGGGCTCGCACGCG
 ACCCATTCTTCCCCTGGAAG
 ATCTCGTGCATCCAGGAGAG
 AAGTTAGAGCGGGAACTGCT
 CTATAGCAACAATAATTACG
 GTGCAATTACGAATGACCAG
 CAGGCTAGTCATGCGGGCTC
 ATAATCCACATGGCTATAGC
 GCTATAACAGCCATCAAAGG
 AGATGTTGGTGCGAAGAAAC
 ATGGTCGAAACTAGCTGCAC
 GGAGAGATTGAATAGAGATA
 CGACAGAGCGAGGCCCTTGA
 TCGCACGCGGTCAACTTGTA
 GAAATCACGCGCATTGTTGT
 TATACCGCAGAAGTTCGGCA
 CAGCATTCAGCGCCCTGGTA
 TTTTGGTGTGGAACCCATTC
 TATAATCCACATGGCTATAG
 ATCACGCGCATTGTTGTCGT
 ATTATAATCCACATGGCTAT
 TGTCGGGTCCGAGTTTGGCC
 AAGTTCGGCAAAGTTAGAGC
 ACGGGAATCCTGGGAGGGCC
 ATTTACGTCCGAGCTATAGC
 CTGGAAGCGCGCTCCCGCCT
 GCAAATGCCTTTCTTTAGGC
 TTACGCATTAACACGACGTT
 AGGTGGTTGTGATCAGCGGC
 GCCCGTGTGAATGTGGAAAT
 GTCCGAGCTATAGCAGCAAA
 AGGTCAAAGGGAGCTATAAC
 GCGGCTGTCGATCTCCAGGA
 TTGCGCTGTATCGTAGCTTC
 AAAGTTAGAGCGGGAACTGC
 TTCCCCTGGAAGCGCGCTCC
 CCCCATGTTCGCGTTTAAGA
 TATCTCAAGAACCCTCTCTC
 CCGCGCCAGTGCCCATCTCG
 GGAACCCATTCTTCCCCTGG
 ATAGCAGCAAAAATTTTGGA
 CGTTTAAGATGAGTGACATC
 TATAACAGCCATCAAAGGAG
 CCAGGAAGATGTTGGTGCGA
 TACGTCACCATTCCCAGCAA
 GCCTTTCTTTAGGCAGCATT
 AACAGCCATCAAAGGAGAGC
 GCATTAACACGACGTTCAGC
 CTCCCGCCTTTATCTCGTGC
 CGTGCATCCAGGAGAGATTG
 CTGGAAACGACTAGATAGAT
 GCATTGTTGTCGTCATGGTT
 CGGCCGGGACAATGGCCCGT
 TTATTAACACGGGCTCATCT
 TAGCAGCAAAAATTTTGGAC
 TCAAGAACCCTCTCTCTACA
 AGTCACATACACAATGCGGC
 CAACGCAAGAGGTCCATTAT
 CGGGCTCGCACGCGGTCAAC
 CTCGCGGGGTGTACCTCGGG
 ATGTGGAAATCGATCGTATA
 AGCTATAACAGCCATCAAAG
 TTAAGGTTAGGGGGTAAGGC
 TCCAATTGGCCGAAATCACG
 AACGACTAGATAGATCCAAT
 GGCCAACCTGAATGTCGGGT
 CCTTTCTTTAGGCAGCATTC
 AGTTGGTACCAACGCAAGAG
 TGTGAATGTGGAAATCGATC
 CATGGTTACAAAATTTACGT
 TTGCTGCTGGAAACGACTAG
 CATGCGGGCTCGCACGCGGT
 CAACAATAATTACGTCACCA
 GAGAGATTGAATAGAGATAT
 GTGCGAAGAAACCGAAATCG
 GGGCTCGCACGCGGTCAACT
 GCAAGAGGTCCATTATTAAC
 GTCACTTGCTGCTGGAAACG
 GGCCGAACCAGGTCAAAGGG
 CGCGCATTGTTGTCGTCATG
 CATTATAATCCACATGGCTA
 GGTGCAATTACGAATGACCA
 GGGAATCCTGGGAGGGCCAA
 CATCTCGGCGAAAAATGGTA
 CGTGTGAATGTGGAAATCGA
 GCTATAGCAACAATAATTAC
 CCGCAGAAGTTCGGCAAAGT
 ACTAGATAGATCCAATTGGC
 AAACAAAGGTGGTTGTGATC
 TCGCGTTTAAGATGAGTGAC
 TCGGGTCCGAGTTTGGCCGA
 AAAATGGTATCTCAAGAACC
 GGACAATGGCCCGTGTGAAT
 GACCAGGCTCAATCGGAGGA
 CAATAATTACGTCACCATTC
 ATCGGTTTGGTCACTTGCTG
 TCGGCGAAAAATGGTATCTC
 AACCCATTCTTCCCCTGGAA
 TCCCGCCTTTATCTCGTGCA
 GATCTCCAGGAAGATGTTGG
 GAAAAATGGTATCTCAAGAA
 GGCCCGTGTGAATGTGGAAA
 GTCCTTCCAGTGCTCGCGGG
 TTGTAACCCGTCGGAACGGG
 ACGCAAGAGGTCCATTATTA
 GCTCGCGGGGTGTACCTCGG
 TAAGGTTAGGGGGTAAGGCC
 CCCCTGGAAGCGCGCTCCCG
 GCTATAGCAGCAAAAATTTT
 TCTCGGCGAAAAATGGTATC
 ATCCAATTGGCCGAAATCAC
 ATGGCCCGTGTGAATGTGGA
 GCCCCTTGCGCTGTATCGTA
 TTGTCGTCATGGTTACAAAA
 AACCGAAATCGTGCCCCATG
 CCAGTGCTCGCGGGGTGTAC
 CCATTATAATCCACATGGCT
 ATGTTGGTGCGAAGAAACCG
 ATGGTTACAAAATTTACGTC
 AGTTTGGCCGAACCAGGTCA
 GTACCAACGCAAGAGGTCCA
 GAGGAGTAGTTGGTACCAAC
 CAAAGTTAGAGCGGGAACTG
 TTAGGGGGTAAGGCCATTTG
 GAAGATGTTGGTGCGAAGAA
 ATGGCTATAGCAACAATAAT
 AAATCACGCGCATTGTTGTC
 TATTCGAGAGTCACATACAC
 AAATGCCTTTCTTTAGGCAG
 CGAATACGACAGAGCGAGGC
 AGATAGATCCAATTGGCCGA
 TGACACGAACACTAAACAAA
 GCCAACCTGAATGTCGGGTC
 CTGCTGCAGGGCTCCCGCGC
 CTCGTGCATCCAGGAGAGAT
 TTTGCCCATTATAATCCACA
 ACGAACACTAAACAAAGGTG
 TGCAGGGCTCCCGCGCCAGT
 AGAAGTTCGGCAAAGTTAGA
 TAGAGATATTCGAGAGTCAC
 CTGCACTATCGGTTTGGTCA
 GGCCATTTGTGCCTTTTTGG
 CACACAGCGTGCCATTCATC
 CAAATGGTCGAAACTAGCTG
 TTACAAAATTTACGTCCGAG
 AACCAGGTCAAAGGGAGCTA
 GCTCAATCGGAGGAGTAGTT
 CCCTGGTAAGTTACGCATTA
 CCGAACCAGGTCAAAGGGAG
 TCCTTCCAGTGCTCGCGGGG
 GCGGGAACTGCTGCAGGGCT
 ACACGAACACTAAACAAAGG
 GGGACAATGGCCCGTGTGAA
 TCAATCGGAGGAGTAGTTGG
 TAAGATGAGTGACATCAAGG
 CCACATGGCTATAGCAACAA
 TGAATAGAGATATTCGAGAG
 AGAGATTGAATAGAGATATT
 ACGGGCTCATCTTTTTGCCC
 CTTTTTGCCCATTATAATCC
 CTCGCACGCGGTCAACTTGT
 CTTCCAGTGCTCGCGGGGTG
 CTCATCTTTTTGCCCATTAT
 AGGCCATTTGTGCCTTTTTG
 AATTTTGGACCGCTGTCCTT
 ATTTGTGCCTTTTTGGTGTG
 ACACGACGTTCAGCGAAGAA
 TTGGTCACTTGCTGCTGGAA
 GTATCGTAGCTTCACAAATG
 ACGCGCATTGTTGTCGTCAT
 CCCTTGCGCTGTATCGTAGC
 GGAAGCGCGCTCCCGCCTTT
 CGTATACCGCAGAAGTTCGG
 AAAGGAGAGCCCCTTGCGCT
 GATGAGTGACATCAAGGTCC
 CGCTGTATCGTAGCTTCACA
 TCACATACACAATGCGGCTG
 AAGAACCCTCTCTCTACAGG
 CAGAGCGAGGCCCTTGACAC
 CCACACAGCGTGCCATTCAT
 GGTCAACTTGTAACCCGTCG
 TATCTCGTGCATCCAGGAGA
 AAGGAGAGCCCCTTGCGCTG
 GGTCCATTATTAACACGGGC
 GTCGATCTCCAGGAAGATGT
 TTAGAGCGGGAACTGCTGCA
 AAAGGTGGTTGTGATCAGCG
 TGGTTGTGATCAGCGGCCGG
 GTTAGAGCGGGAACTGCTGC
 CCAACCTGAATGTCGGGTCC
 GTTCAGCGAAGAACGAATAC
 CTCCCGCGCCAGTGCCCATC
 TCGTGCATCCAGGAGAGATT
 CGCGGGGTGTACCTCGGGCT
 CACTAAACAAAGGTGGTTGT
 CCCTTGACACGAACACTAAA
 CGGTTTGGTCACTTGCTGCT
 ACTATCGGTTTGGTCACTTG
 TGGAAACGACTAGATAGATC
 GTGGTGCAATTACGAATGAC
 TGGTGCAATTACGAATGACC
 GACGTTCAGCGAAGAACGAA
 AATCGATCGTATACCGCAGA
 TTTGTGCCTTTTTGGTGTGG
 CATTCAGCGCCCTGGTAAGT
 GCGCCAGTGCCCATCTCGGC
 GTAACCCGTCGGAACGGGAA
 AACTGCTGCAGGGCTCCCGC
 AGAGATATTCGAGAGTCACA
 GTCCCACACAGCGTGCCATT
 AGCTATAGCAGCAAAAATTT
 TTTTGGACCGCTGTCCTTCC
 TCGGAGGAGTAGTTGGTACC
 CTAGCTGCACTATCGGTTTG
 TCCAGGAAGATGTTGGTGCG
 AGATTGAATAGAGATATTCG
 CAGGAAGATGTTGGTGCGAA
 TCAAAGGAGAGCCCCTTGCG
 CCATTATTAACACGGGCTCA
 AAGGGAGCTATAACAGCCAT
 CTATAACAGCCATCAAAGGA
 AAGGTGGTTGTGATCAGCGG
 GAGGGCCAACCTGAATGTCG
 GCGAAAAATGGTATCTCAAG
 TTATAATCCACATGGCTATA
 AGGCTCAATCGGAGGAGTAG
 TGCGGGCTCGCACGCGGTCA
 TCACTTGCTGCTGGAAACGA
 AGGGAGCTATAACAGCCATC
 GGACCGCTGTCCTTCCAGTG
 TTCACAAATGGTCGAAACTA
 TAACACGACGTTCAGCGAAG
 CCGTGTGAATGTGGAAATCG
 CGGGCTTTAAGGTTAGGGGG
 TTGTGATCAGCGGCCGGGAC
 GTGACATCAAGGTCCCACAC
 TGGCCGAACCAGGTCAAAGG
 GACCGCTGTCCTTCCAGTGC
 TTCTTCCCCTGGAAGCGCGC
 GTCGAAACTAGCTGCACTAT
 TACGTCCGAGCTATAGCAGC
 CCTTGCGCTGTATCGTAGCT
 CGGTCAACTTGTAACCCGTC
 CAGTGCCCATCTCGGCGAAA
 GCTTCACAAATGGTCGAAAC
 GGTGGTTGTGATCAGCGGCC
 TGTGCCTTTTTGGTGTGGAA
 GGCTCCCGCGCCAGTGCCCA
 TGTGGAACCCATTCTTCCCC
 TCTTTTTGCCCATTATAATC
 CTTTATCTCGTGCATCCAGG
 AACGAATACGACAGAGCGAG
 GATGTTGGTGCGAAGAAACC
 TGCCCATTATAATCCACATG
 AATCGGAGGAGTAGTTGGTA
 GGGTAAGGCCATTTGTGCCT
 GTTTGGCCGAACCAGGTCAA
 TCTCTACAGGCTAGTCATGC
 GAAGAACGAATACGACAGAG
 CGCGCTCCCGCCTTTATCTC
 AATCCACATGGCTATAGCAA
 CTTTTTGGTGTGGAACCCAT
 AGCGCGCTCCCGCCTTTATC
 GAGCTATAGCAGCAAAAATT
 AGCAAAAATTTTGGACCGCT
 TAGTTGGTACCAACGCAAGA
 CAAAGGAGAGCCCCTTGCGC
 ACAGGCTAGTCATGCGGGCT
 GAGAGCCCCTTGCGCTGTAT
 GTTTGGTCACTTGCTGCTGG
 ATTATTAACACGGGCTCATC
 GAAACTAGCTGCACTATCGG
 GCTGTCCTTCCAGTGCTCGC
 TAAACAAAGGTGGTTGTGAT
 CGTCACCATTCCCAGCAAAT
 TCCGAGCTATAGCAGCAAAA
 GGTGTGGAACCCATTCTTCC
 ACCGCAGAAGTTCGGCAAAG
 GGTATCTCAAGAACCCTCTC
 CGCTGTCCTTCCAGTGCTCG
 CATTTGTGCCTTTTTGGTGT
 CTCTCTACAGGCTAGTCATG
 CAGCGCCCTGGTAAGTTACG
 GCCTTTATCTCGTGCATCCA
 ACTTGCTGCTGGAAACGACT
 AACCCGTCGGAACGGGAATC
 CCGAGTTTGGCCGAACCAGG
 CTGGGAGGGCCAACCTGAAT
 GGTCACTTGCTGCTGGAAAC
 CTCCAGGAAGATGTTGGTGC
 CGCGGTCAACTTGTAACCCG
 CACTATCGGTTTGGTCACTT
 GTCATGGTTACAAAATTTAC
 AAGATGTTGGTGCGAAGAAA
 GCAGGGCTCCCGCGCCAGTG
 CTGTCGATCTCCAGGAAGAT
 TTCTTTAGGCAGCATTCAGC
 CACGCGGTCAACTTGTAACC
 TGCCTTTTTGGTGTGGAACC
 GAAATCGATCGTATACCGCA
 AGGCAGCATTCAGCGCCCTG
 GCACGCGGTCAACTTGTAAC
 CAGGGCTCCCGCGCCAGTGC
 TTTAAGATGAGTGACATCAA
 CACGCGCATTGTTGTCGTCA
 GAGTTTGGCCGAACCAGGTC
 ACCGAAATCGTGCCCCATGT
 AGGTCCATTATTAACACGGG
 CAAGAACCCTCTCTCTACAG
 TTTGGTCACTTGCTGCTGGA
 CTTGCTGCTGGAAACGACTA
 ACACAATGCGGCTGTCGATC
 GTTACGCATTAACACGACGT
 AACTTGTAACCCGTCGGAAC
 AGCCATCAAAGGAGAGCCCC
 GCTGTCGATCTCCAGGAAGA
 CAAAGGGAGCTATAACAGCC
 TGGGAGGGCCAACCTGAATG
 GACTAGATAGATCCAATTGG
 TTGTGCCTTTTTGGTGTGGA
 GCGTTTAAGATGAGTGACAT
 CGGGGTGTACCTCGGGCTTT
 GCGCGCTCCCGCCTTTATCT
 ATGCGGCTGTCGATCTCCAG
 CGCAGAAGTTCGGCAAAGTT
 ATGACCAGGCTCAATCGGAG
 CATCAAAGGAGAGCCCCTTG
 ATAGAGATATTCGAGAGTCA
 TGCTCGCGGGGTGTACCTCG
 TTGGTACCAACGCAAGAGGT
 AGCATTCAGCGCCCTGGTAA
 AGGGCTCCCGCGCCAGTGCC
 AACTAGCTGCACTATCGGTT
 CAATCGGAGGAGTAGTTGGT
 GTTCGCGTTTAAGATGAGTG
 GTAGCTTCACAAATGGTCGA
 CATTGTTGTCGTCATGGTTA
 GGGGTAAGGCCATTTGTGCC
 CGAAAAATGGTATCTCAAGA
 ATCAGCGGCCGGGACAATGG
 CTGTCCTTCCAGTGCTCGCG
 GGGAGGGCCAACCTGAATGT
 TCACGCGCATTGTTGTCGTC
 GATCGTATACCGCAGAAGTT
 AGCGCCCTGGTAAGTTACGC
 TAAGTTACGCATTAACACGA
 CCGAGCTATAGCAGCAAAAA
 TAGAGCGGGAACTGCTGCAG
 ACATCAAGGTCCCACACAGC
 ATCGATCGTATACCGCAGAA
 GTGGAACCCATTCTTCCCCT
 ATTAACACGACGTTCAGCGA
 CGGCGAAAAATGGTATCTCA
 TAACAGCCATCAAAGGAGAG
 TGCCCATCTCGGCGAAAAAT
 AATAGAGATATTCGAGAGTC
 AAGCGCGCTCCCGCCTTTAT
 CTTTAGGCAGCATTCAGCGC
 GCACTATCGGTTTGGTCACT
 GGCTTTAAGGTTAGGGGGTA
 GAGATATTCGAGAGTCACAT
 TCAGCGAAGAACGAATACGA
 AAATTTACGTCCGAGCTATA
 GTGGAAATCGATCGTATACC
 GCCCATTATAATCCACATGG
 TAAGGCCATTTGTGCCTTTT
 CTTTCTTTAGGCAGCATTCA
 CTGTATCGTAGCTTCACAAA
 TTGGTGTGGAACCCATTCTT
 GGAGCTATAACAGCCATCAA
 TTCGCGTTTAAGATGAGTGA
 AGGGGGTAAGGCCATTTGTG
 TGAATGTGGAAATCGATCGT
 ACGCATTAACACGACGTTCA
 ATTAACACGGGCTCATCTTT
 AGGAAGATGTTGGTGCGAAG
 GAGCGGGAACTGCTGCAGGG
 AATGGTATCTCAAGAACCCT
 CTACAGGCTAGTCATGCGGG
 CCAGGAGAGATTGAATAGAG
 CGAAGAAACCGAAATCGTGC
 GAACTGCTGCAGGGCTCCCG
 ACCAGGCTCAATCGGAGGAG
 TATCGGTTTGGTCACTTGCT
 TTTTGCCCATTATAATCCAC
 TTCAGCGAAGAACGAATACG
 GGCTCGCACGCGGTCAACTT
 TCACCATTCCCAGCAAATGC
 TGCGAAGAAACCGAAATCGT
 AGAGGTCCATTATTAACACG
 GGCGAAAAATGGTATCTCAA
 CACAATGCGGCTGTCGATCT
 TACCAACGCAAGAGGTCCAT
 TACACAATGCGGCTGTCGAT
 CACGAACACTAAACAAAGGT
 GAACACTAAACAAAGGTGGT
 CTCAATCGGAGGAGTAGTTG
 CGCATTGTTGTCGTCATGGT
 AGATATTCGAGAGTCACATA
 ACCTGAATGTCGGGTCCGAG
 TTACGAATGACCAGGCTCAA
 GCCCCATGTTCGCGTTTAAG
 AGCTTCACAAATGGTCGAAA
 GAACGGGAATCCTGGGAGGG
 CGGGAACTGCTGCAGGGCTC
 TGGTCGAAACTAGCTGCACT
 TCGATCTCCAGGAAGATGTT
 CCATTCTTCCCCTGGAAGCG
 AAGATGAGTGACATCAAGGT
 CATTCCCAGCAAATGCCTTT
 TCCACATGGCTATAGCAACA
 GCTCCCGCGCCAGTGCCCAT
 CGGCAAAGTTAGAGCGGGAA
 CTTTAAGGTTAGGGGGTAAG
 CCCATCTCGGCGAAAAATGG
 CCATTTGTGCCTTTTTGGTG
 GCTGTATCGTAGCTTCACAA
 CCTGGAAGCGCGCTCCCGCC
 AAACTAGCTGCACTATCGGT
 AGAACCCTCTCTCTACAGGC
 CGGGACAATGGCCCGTGTGA
 CATTATTAACACGGGCTCAT
 GCGCATTGTTGTCGTCATGG
 CTCGGCGAAAAATGGTATCT
 AACGCAAGAGGTCCATTATT
 ACGACGTTCAGCGAAGAACG
 GCTGGAAACGACTAGATAGA
 ACATGGCTATAGCAACAATA
 CGGGAATCCTGGGAGGGCCA
 CAAATGCCTTTCTTTAGGCA
 TCGTCATGGTTACAAAATTT
 TAGGGGGTAAGGCCATTTGT
 GCAGCAAAAATTTTGGACCG
 TTTGGTGTGGAACCCATTCT
 ACGTCCGAGCTATAGCAGCA
 ATGTCGGGTCCGAGTTTGGC
 CTAGATAGATCCAATTGGCC
 GTTGGTGCGAAGAAACCGAA
 CGCAAGAGGTCCATTATTAA
 GGCTATAGCAACAATAATTA
 AAGAAACCGAAATCGTGCCC
 GCCAGTGCCCATCTCGGCGA
 AAACCGAAATCGTGCCCCAT
 GGGCTCATCTTTTTGCCCAT
 GCCGAACCAGGTCAAAGGGA
 TTATCTCGTGCATCCAGGAG
 AAGGCCATTTGTGCCTTTTT
 TGTGATCAGCGGCCGGGACA
 GTCACATACACAATGCGGCT
 GGCAAAGTTAGAGCGGGAAC
 CGCCAGTGCCCATCTCGGCG
 ACGCGGTCAACTTGTAACCC
 GCTCATCTTTTTGCCCATTA
 CGAACCAGGTCAAAGGGAGC
 TATCGTAGCTTCACAAATGG
 GAGTCACATACACAATGCGG
 AGAGCCCCTTGCGCTGTATC
 ATCAAGGTCCCACACAGCGT
 TAGTCATGCGGGCTCGCACG
 GTTAGGGGGTAAGGCCATTT
 CAATGGCCCGTGTGAATGTG
 GCGAGGCCCTTGACACGAAC
 TCAAAGGGAGCTATAACAGC
 CAAGAGGTCCATTATTAACA
 TCTCCAGGAAGATGTTGGTG
 TCCCGCGCCAGTGCCCATCT
 AATCACGCGCATTGTTGTCG
 ATCTCGGCGAAAAATGGTAT
 AATGTCGGGTCCGAGTTTGG
 TCAAGGTCCCACACAGCGTG
 GGTACCAACGCAAGAGGTCC
 CGTCATGGTTACAAAATTTA
 GACAGAGCGAGGCCCTTGAC
 GGAAGATGTTGGTGCGAAGA
 AACACGGGCTCATCTTTTTG
 CTATAGCAGCAAAAATTTTG
 ATGGTATCTCAAGAACCCTC
 TGTGGAAATCGATCGTATAC
 TGCCTTTCTTTAGGCAGCAT
 TCGGTTTGGTCACTTGCTGC
 TGGTACCAACGCAAGAGGTC
 CGAATGACCAGGCTCAATCG
 TTGGACCGCTGTCCTTCCAG
 TGTTGTCGTCATGGTTACAA
 TAGGCAGCATTCAGCGCCCT
 GCCCATCTCGGCGAAAAATG
 ACAATAATTACGTCACCATT
 TACAAAATTTACGTCCGAGC
 AATTGGCCGAAATCACGCGC
 TTTGGACCGCTGTCCTTCCA
 GCGGGGTGTACCTCGGGCTT
 GCAGAAGTTCGGCAAAGTTA
 CCCGCCTTTATCTCGTGCAT
 CAAAATTTACGTCCGAGCTA
 CCATCTCGGCGAAAAATGGT
 TGAATGTCGGGTCCGAGTTT
 TCCTGGGAGGGCCAACCTGA
 TCCGAGTTTGGCCGAACCAG
 AGGCTAGTCATGCGGGCTCG
 TATTAACACGGGCTCATCTT
 GCTGCACTATCGGTTTGGTC
 TATAGCAACAATAATTACGT
 GTTACAAAATTTACGTCCGA
 GGGTCCGAGTTTGGCCGAAC
 GCCTTTTTGGTGTGGAACCC
 AGGAGAGATTGAATAGAGAT
 TGGTGTGGAACCCATTCTTC
 ACAATGGCCCGTGTGAATGT
 TAACCCGTCGGAACGGGAAT
 AGTTACGCATTAACACGACG
 CAGGAGAGATTGAATAGAGA
 GCGCTGTATCGTAGCTTCAC
 GCTCGCACGCGGTCAACTTG
 GGTGCGAAGAAACCGAAATC
 ATGCGGGCTCGCACGCGGTC
 GGTGTACCTCGGGCTTTAAG
 TACCGCAGAAGTTCGGCAAA
 GTGCCCCATGTTCGCGTTTA
 GTAAGGCCATTTGTGCCTTT
 GCCCTTGACACGAACACTAA
 GAACCAGGTCAAAGGGAGCT
 TTACGTCCGAGCTATAGCAG
 ATGAGTGACATCAAGGTCCC
 ACCAACGCAAGAGGTCCATT
 ATCAAAGGAGAGCCCCTTGC
 ATTACGTCACCATTCCCAGC
 TCACAAATGGTCGAAACTAG
 ACATACACAATGCGGCTGTC
 ACCATTCCCAGCAAATGCCT
 AGCTGCACTATCGGTTTGGT
 CAGCAAAAATTTTGGACCGC
 GTGGTTGTGATCAGCGGCCG
 TGGAACCCATTCTTCCCCTG
 AGAGTCACATACACAATGCG
 TAGCTGCACTATCGGTTTGG
 CTAAACAAAGGTGGTTGTGA
 AGTTAGAGCGGGAACTGCTG
 GTTGTGATCAGCGGCCGGGA
 CGTCGGAACGGGAATCCTGG
 CACCATTCCCAGCAAATGCC
 CCTTTTTGGTGTGGAACCCA
 AAATTTTGGACCGCTGTCCT
 CATGGCTATAGCAACAATAA
 TCGAAACTAGCTGCACTATC
 AAAGGGAGCTATAACAGCCA
 ATATTCGAGAGTCACATACA
 AAAAATTTTGGACCGCTGTC
 TTAACACGACGTTCAGCGAA
 TCGTATACCGCAGAAGTTCG
 CGAACACTAAACAAAGGTGG
 AGCAGCAAAAATTTTGGACC
 AGTTCGGCAAAGTTAGAGCG
 TTCCCAGCAAATGCCTTTCT
 ATTCGAGAGTCACATACACA
 GTTGTCGTCATGGTTACAAA
 GGGGGTAAGGCCATTTGTGC
 TTCGGCAAAGTTAGAGCGGG
 AACAAAGGTGGTTGTGATCA
 TGCTGCAGGGCTCCCGCGCC
 TGGTAAGTTACGCATTAACA
 CTTGACACGAACACTAAACA
 CCATCAAAGGAGAGCCCCTT
 AGCGAAGAACGAATACGACA
 TTGGCCGAACCAGGTCAAAG
 TTTATCTCGTGCATCCAGGA
 CTCGGGCTTTAAGGTTAGGG
 CGTAGCTTCACAAATGGTCG
 TTACGTCACCATTCCCAGCA
 GGAAACGACTAGATAGATCC
 CGAGGCCCTTGACACGAACA
 ACCTCGGGCTTTAAGGTTAG
 TCCCACACAGCGTGCCATTC
 TTTTTGCCCATTATAATCCA
 AGCAAATGCCTTTCTTTAGG
 CGATCGTATACCGCAGAAGT
--- a/chapter3/populate_templates.py
+++ b/chapter3/populate_templates.py
@ -0,0 +1,49 @@
 import jinja2
 import os
 def main():
    # Jinja env
    env = jinja2.Environment(loader=jinja2.FileSystemLoader('.'))
    problems = [
        {
            'chapter': '3',
            'problem': 'a',
            'title': 'Generate k-mer Composition of a String',
            'description': 'Given an input string, generate a list of all kmers that are in the input string.',
            'url': 'http://rosalind.info/problems/ba3a/'
        },
        {
            'chapter': '3',
            'problem': 'b',
            'title': 'Reconstruct string from genome path',
            'description': 'Reconstruct a string from its genome path, i.e., sequential fragments of overlapping DNA.',
            'url': 'http://rosalind.info/problems/ba3b/'
        },
        {
            'chapter': '3',
            'problem': 'c',
            'title': 'Construct the overlap graph of a set of k-mers',
            'description': 'Given a set of overlapping k-mers, construct the overlap graph and print a sorted adjacency matrix',
            'url': 'http://rosalind.info/problems/ba3c/'
        },
    ]
    print("Writing problem boilerplate code")
    t = 'template.go.j2'
    for problem in problems:
        contents = env.get_template(t).render(**problem)
        fname = 'ba'+problem['chapter']+problem['problem']+'.go'
        if not os.path.exists(fname):
            print("Writing to file %s..."%(fname))
            with open(fname,'w') as f:
                f.write(contents)
        else:
            print("File %s already exists, skipping..."%(fname))
    print("Done")
 if __name__=="__main__":
    main()
--- a/chapter3/template.go.j2
+++ b/chapter3/template.go.j2
@ -0,0 +1,49 @@
 package rosalindchapter{{chapter}}
 import (
 	"fmt"
 	"log"
 	rosa "github.com/charlesreid1/go-rosalind/rosalind"
 )
 // Print problem description for Rosalind.info
 // Problem BA{{chapter}}{{problem}}: {{title}}
 func BA{{chapter}}{{problem}}Description() {
 	description := []string{
 		"-----------------------------------------",
 		"Rosalind: Problem BA{{chapter}}{{problem}}:",
 		"{{title}}",
 		"",
 		"{{description}}",
 		"",
 		"URL: {{url}}",
 		"",
 	}
 	for _, line := range description {
 		fmt.Println(line)
 	}
 }
 // Run the problem
 func BA{{chapter}}{{problem}}(filename string) {
 	BA{{chapter}}{{problem}}Description()
 	// Read the contents of the input file
 	// into a single string
 	lines, err := rosa.ReadLines(filename)
 	if err != nil {
 		log.Fatalf("rosa.ReadLines: %v", err)
 	}
 	//// Input file contents
 	//input := lines[0]
 	//params := lines[1]
 	//result := rosa.PatternCount(input, pattern)
 	// 
 	//fmt.Println("")
 	//fmt.Printf("Computed result from input file: %s\n", filename)
 	//fmt.Println(result)
 }
--- a/rosalind/Readme.md
+++ b/rosalind/Readme.md
@ -0,0 +1,4 @@
 # rosalind go package
 This directory contains the `rosalind` Go package.
--- a/chapter01/data/clump_finding.txt
+++ b/chapter01/data/clump_finding.txt
--- a/chapter01/data/frequent_words.txt
+++ b/chapter01/data/frequent_words.txt
--- a/rosalind/data/frequent_words_mismatch.txt
+++ b/rosalind/data/frequent_words_mismatch.txt
@ -0,0 +1,5 @@
 Input:
 CACAGTAGGCGCCGGCACACACAGCCCCGGGCCCCGGGCCGCCCCGGGCCGGCGGCCGCCGGCGCCGGCACACCGGCACAGCCGTACCGGCACAGTAGTACCGGCCGGCCGGCACACCGGCACACCGGGTACACACCGGGGCGCACACACAGGCGGGCGCCGGGCCCCGGGCCGTACCGGGCCGCCGGCGGCCCACAGGCGCCGGCACAGTACCGGCACACACAGTAGCCCACACACAGGCGGGCGGTAGCCGGCGCACACACACACAGTAGGCGCACAGCCGCCCACACACACCGGCCGGCCGGCACAGGCGGGCGGGCGCACACACACCGGCACAGTAGTAGGCGGCCGGCGCACAGCC
 10 2
 Output:
 GCACACAGAC GCGCACACAC
--- a/rosalind/data/frequent_words_mismatch_complements.txt
+++ b/rosalind/data/frequent_words_mismatch_complements.txt
@ -0,0 +1,5 @@
 Input
 CTTGCCGGCGCCGATTATACGATCGCGGCCGCTTGCCTTCTTTATAATGCATCGGCGCCGCGATCTTGCTATATACGTACGCTTCGCTTGCATCTTGCGCGCATTACGTACTTATCGATTACTTATCTTCGATGCCGGCCGGCATATGCCGCTTTAGCATCGATCGATCGTACTTTACGCGTATAGCCGCTTCGCTTGCCGTACGCGATGCTAGCATATGCTAGCGCTAATTACTTAT
 9 3
 Output
 AGCGCCGCT AGCGGCGCT
--- a/rosalind/data/genome_path_string.txt
+++ b/rosalind/data/genome_path_string.txt
--- a/chapter01/data/hamming_distance.txt
+++ b/chapter01/data/hamming_distance.txt
--- a/chapter01/data/minimum_skew.txt
+++ b/chapter01/data/minimum_skew.txt
--- a/rosalind/data/motif_enumeration.txt
+++ b/rosalind/data/motif_enumeration.txt
@ -0,0 +1,10 @@
 Input
 5 2
 TCTGAGCTTGCGTTATTTTTAGACC
 GTTTGACGGGAACCCGACGCCTATA
 TTTTAGATTTCCTCAGTCCACTATA
 CTTACAATTTCGTTATTTATCTAAT
 CAGTAGGAATAGCCACTTTGTTGTA
 AAATCCATTAAGGAAAGACGACCGT
 Output
 AAACT AAATC AACAC AACAT AACCT AACTA AACTC AACTG AACTT AAGAA AAGCT AAGGT AAGTC AATAC AATAT AATCC AATCT AATGC AATTC AATTG ACAAC ACACA ACACC ACACG ACACT ACAGA ACAGC ACATC ACATG ACCAT ACCCT ACCGT ACCTA ACCTC ACCTG ACCTT ACGAC ACGAG ACGAT ACGCT ACGGT ACGTC ACGTT ACTAA ACTAG ACTAT ACTCA ACTCC ACTCG ACTCT ACTGA ACTGC ACTGT ACTTA ACTTC ACTTT AGAAA AGAAC AGAAG AGAAT AGACA AGACT AGATA AGATC AGCAT AGCCA AGCGT AGCTA AGCTC AGCTG AGCTT AGGAT AGGTA AGGTC AGTAA AGTAC AGTAT AGTCC AGTCG AGTCT AGTGA AGTTG ATAAA ATAAC ATACA ATACC ATAGA ATATA ATATC ATATG ATATT ATCAG ATCCC ATCCG ATCCT ATCGA ATCGC ATCTA ATCTC ATCTG ATGAC ATGAT ATGCA ATGCC ATGGA ATGGC ATGTA ATGTC ATTAA ATTAC ATTAG ATTAT ATTCA ATTCC ATTCG ATTGA ATTGC ATTGG ATTGT ATTTA ATTTC ATTTG ATTTT CAAAG CAACC CAACT CAAGA CAAGC CAATA CAATT CACAC CACAG CACCT CACGT CACTA CACTT CAGAA CAGAC CAGAT CAGGT CAGTA CAGTC CATAA CATAC CATAG CATAT CATCC CATCT CATGA CATGT CATTA CATTG CATTT CCAAG CCATA CCATG CCATT CCCGT CCCTA CCCTT CCGAA CCGAC CCGAT CCGCT CCGGT CCGTA CCGTC CCGTG CCGTT CCTAC CCTAT CCTCA CCTCC CCTTA CCTTC CCTTG CCTTT CGAAA CGAAG CGACA CGACT CGAGT CGATA CGATG CGATT CGCAA CGCAT CGCCA CGCGA CGCTA CGCTC CGCTT CGGAC CGGAT CGGCA CGGTA CGGTC CGGTT CGTAA CGTAC CGTCA CGTCG CGTCT CGTTA CGTTT CTAAC CTAAG CTAAT CTACA CTACC CTACG CTACT CTAGA CTAGC CTAGG CTAGT CTATA CTATC CTATG CTATT CTCAT CTCCG CTCGT CTCTA CTCTT CTGAA CTGAG CTGCA CTGCC CTGTA CTGTT CTTAA CTTAC CTTAG CTTAT CTTCA CTTGA CTTTA CTTTC CTTTG CTTTT GAAAT GAACA GAACT GAAGT GAATG GAATT GACAC GACAT GACCA GACCT GACGT GACTT GAGAA GAGAT GAGCT GATAA GATAC GATAG GATAT GATCA GATCC GATCG GATCT GATGT GATTA GATTC GATTG GATTT GCAAT GCACT GCATC GCATT GCCAT GCCGT GCCTA GCCTT GCGAT GCGGT GCGTC GCGTT GCTAA GCTAC GCTAG GCTAT GCTGA GCTGT GCTTA GCTTT GGAAT GGACA GGATA GGATC GGATT GGCTA GGGAT GGTAC GGTAG GGTAT GGTCA GGTCG GGTTA GTAAA GTAAG GTACA GTACC GTACG GTAGA GTATA GTATC GTATG GTATT GTCAA GTCAG GTCCG GTCCT GTCGA GTCGC GTCGT GTCTA GTCTG GTGAA GTGAG GTGCA GTGCG GTTAA GTTAC GTTAG GTTAT GTTCA GTTCC GTTCG GTTGA GTTTA TAAAC TAAAG TAACA TAACC TAACT TAAGA TAAGC TAATA TAATC TACAC TACAG TACCC TACCG TACCT TACGA TACGC TACGT TACTA TACTC TACTG TAGAA TAGAC TAGAG TAGAT TAGCC TAGCG TAGGA TAGTC TATAA TATAC TATAT TATCA TATCC TATCG TATGA TATGC TATGG TATGT TATTA TATTG TCAAC TCAAT TCACC TCACG TCACT TCAGA TCATA TCATG TCCAA TCCAC TCCAG TCCAT TCCCA TCCCT TCCGA TCCGC TCCGT TCCTA TCCTG TCCTT TCGAA TCGAC TCGAT TCGCC TCGCT TCGGA TCGGC TCGGG TCGGT TCGTC TCTAC TCTAG TCTAT TCTCC TCTCT TCTGG TCTGT TCTTA TCTTT TGAAA TGAAC TGAAT TGACA TGACC TGACT TGAGA TGAGC TGAGT TGATA TGATC TGATG TGATT TGCAA TGCAC TGCAG TGCAT TGCCA TGCCG TGCCT TGCGA TGCGT TGCTT TGGAA TGGAT TGGTA TGTAA TGTAG TGTAT TGTCC TGTCG TGTGG TGTTA TTAAA TTAAC TTAAG TTAAT TTACA TTACC TTACG TTACT TTAGA TTAGC TTAGG TTAGT TTATA TTATC TTATG TTATT TTCAA TTCAC TTCAT TTCCA TTCCC TTCCT TTCGA TTCGG TTCGT TTCTA TTCTG TTGAA TTGAC TTGAG TTGAT TTGCA TTGCG TTGGA TTGGG TTGTG TTTAA TTTAC TTTAG TTTAT TTTCA TTTCC TTTCG TTTGA TTTGG TTTTA TTTTG
--- a/rosalind/data/neighbors.txt
+++ b/rosalind/data/neighbors.txt
--- a/rosalind/data/number_to_pattern.txt
+++ b/rosalind/data/number_to_pattern.txt
@ -0,0 +1,5 @@
 Input
 5353
 7
 Output
 CCATGGC
--- a/rosalind/data/overlap_graph.txt
+++ b/rosalind/data/overlap_graph.txt
--- a/chapter01/data/pattern_count.txt
+++ b/chapter01/data/pattern_count.txt
--- a/chapter01/data/pattern_matching.txt
+++ b/chapter01/data/pattern_matching.txt
--- a/rosalind/data/pattern_to_number.txt
+++ b/rosalind/data/pattern_to_number.txt
@ -0,0 +1,4 @@
 Input
 CTTCTCACGTACAACAAAATC
 Output
 2161555804173
--- a/chapter01/data/reverse_complement.txt
+++ b/chapter01/data/reverse_complement.txt
--- a/rosalind/data/string_composition.txt
+++ b/rosalind/data/string_composition.txt
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Charles Reid	9092f98bf6	Add solution to BA2F (#17 ) * add a maxint and minint utility function * add problems ba2f and ba2g * remove ba2g for now * adding BA2f to chapter 2 problems * add BA2f solution (failing) * remove expensive test * fix random motif generator script (random number problems) * fix how we aggregate over multiple random motif searches * call random motif search multiple times * update BA2F so eet wurk * make tests a lil easier * add ba2f input file, whoops * add ba2g - gibbs sampler * update BA2g solution with bug fixes * add ba2g to chapter 2 tests. add ba2g input file.	6 years ago
Charles Reid	2a580cbdc7	add a maxint and minint utility function (#16 )	6 years ago
Charles Reid	4810449c86	Fix BA2e solution (#14 ) * add materials for BA2D (in progress) * add another test of first inner iteration - helped uncover multiple bugs * fix build error * add final, working BA2D solution * add solution to BA2E * greedy algorithm should extract kmers in the order in which they occur	6 years ago
Charles Reid	216872f46b	Add solution to BA2E (#12 ) * add materials for BA2D (in progress) * add another test of first inner iteration - helped uncover multiple bugs * fix build error * add final, working BA2D solution * add solution to BA2E	6 years ago
Charles Reid	49d7385a4c	add materials for BA2D (in progress) (#11 ) * add materials for BA2D (in progress) * add another test of first inner iteration - helped uncover multiple bugs * fix build error * add final, working BA2D solution	6 years ago
Charles Reid	10b2a14f54	Add BA2c solution (#10 ) * add chapter3 module, and rosalind functions for BA3a * add test for genome reconstruction * update shields to include godoc * spacing * improved function name * add file test ReconstructGenomeFromPath * add data file for ReconstructGenomeFromPath file test * add a strings.Trim(_," ") to fix failing test * update and fix string composition test * add BA3B problems * add ba3b problem to chapter 3 test * add ba3b into populate templates script * add chapter3 to travis ci * add graph data structure for BA3C * add graph data structure and function to create overlap graph * add file-based test for BA3C overlap graph * add BA3c to chapter 3 tests * add BA3C to templates list * add BA3c problem to chapter 3 module * add problem BA2c to chapter 2 problems and tests * cover BA2c with new rosalind function. add tests * add version that passes on rosalind	6 years ago
Charles Reid	a0c9f211bb	add chapter3 module, and rosalind functions for BA3a thru BA3c (#9 ) * add chapter3 module, and rosalind functions for BA3a * add test for genome reconstruction * update shields to include godoc * spacing * improved function name * add file test ReconstructGenomeFromPath * add data file for ReconstructGenomeFromPath file test * add a strings.Trim(_," ") to fix failing test * update and fix string composition test * add BA3B problems * add ba3b problem to chapter 3 test * add ba3b into populate templates script * add chapter3 to travis ci * add graph data structure for BA3C * add graph data structure and function to create overlap graph * add file-based test for BA3C overlap graph * add BA3c to chapter 3 tests * add BA3C to templates list * add BA3c problem to chapter 3 module	6 years ago
Charles Reid	87eac56bc4	Add Stronghold module (#8 ) * fix up error messages in ba1 functions * add two supporting hamming distance min functions for median string question BA2B * fix MinKmerDistance algorithm to be faster * add script to generate static site documentation from godoc tool * update gitignore * adding rosalind stronghold functions and tests * add median string functionality for ba2b * add stronghold go jinja template, plus data set for dna question * mention the stronghold dir in the readme	6 years ago
Charles Reid	8543defb86	Continue work on Chapter 2 problems (#7 ) * fix up error messages in ba1 functions * add two supporting hamming distance min functions for median string question BA2B * fix MinKmerDistance algorithm to be faster * add script to generate static site documentation from godoc tool * update gitignore * adding rosalind stronghold functions and tests * add median string functionality for ba2b * add output to readme * fix ba2b * add BA2b test * fix test template and calls * add ba2b driver * ba2b in the bag	6 years ago
Charles Reid	2a64f89e35	Add code for Chapter 2 (#6 ) * update readme to be a little more clear * add ba2{a,b,c} code, plus jinja template for boilerplate code * add chapter02 test * move chapter01 -> chapter1 * move chapter2 chapter02 * improve error handling * add ba2 functionality tests * comment out long test (for convenience) * add BA2 function and test - motif enumeration * update readme a bit * rename functions to lowercase letter * rename test * include more debug tests * remove vendored rosalind.go, prepare to remove vendored utils * update documentation/quickstart/readme for chapter1 and chapter2 * add example input for ba2a * fix chapter1, add chapter2 to travis tests	6 years ago
Charles Reid	8992e3e3ce	Merge branch 'chapter1cleanup' * chapter1cleanup: shield links add language shield. shields up. add MIT license add license shield fix (remove) custom travis go import path add CheckIsDNA to BA1A tests for chapter01 working update readme to reflect chapter 1 cleanup add chapter01 tests to travis file clean up chapter 1, consolidate tests	6 years ago
Charles Reid	61b538675d	Merge branch 'master' of github.com:charlesreid1/go-rosalind into chapter1cleanup * 'master' of github.com:charlesreid1/go-rosalind: clean up chapter 1, consolidate tests (#5)	6 years ago
Charles Reid	e7b887b94a	shield links	6 years ago
Charles Reid	385bd4ac58	add language shield. shields up.	6 years ago
Charles Reid	cf22c98e2b	clean up chapter 1, consolidate tests (#5 ) * clean up chapter 1, consolidate tests * add chapter01 tests to travis file * update readme to reflect chapter 1 cleanup * tests for chapter01 working * add CheckIsDNA to BA1A * fix (remove) custom travis go import path * add license shield * add MIT license	6 years ago
Charles Reid	ef2172d04c	add MIT license	6 years ago
Charles Reid	b971d2d1f9	add license shield	6 years ago
Charles Reid	257bdd3f5b	fix (remove) custom travis go import path	6 years ago
Charles Reid	f70724b137	add CheckIsDNA to BA1A	6 years ago
Charles Reid	ef412f12f0	tests for chapter01 working	6 years ago
Charles Reid	3a2b8d65af	update readme to reflect chapter 1 cleanup	6 years ago
Charles Reid	d8efc0df41	add chapter01 tests to travis file	6 years ago
Charles Reid	42f5d6f5fd	clean up chapter 1, consolidate tests	6 years ago
Charles Reid	6a5d827185	yikes, spaces	6 years ago
Charles Reid	d3782ad84d	fix tab	6 years ago
Charles Reid	d4cf42824e	fix import statements in readme example	6 years ago
Charles Reid	8f24f5f75c	fix typo in readme example	6 years ago
Charles Reid	60abfd5288	fix typo in .travis.yml	6 years ago
Charles Reid	1695a36aa4	Make this go get friendly (#3 ) * add rosalind package that will be go get friendly * update readme with new structure and approach * moving data to rosalind dir * add travis.yml file	6 years ago
Charles Reid	7adf5b5418	Chapter1 part2 (#2 ) * added init version of entire BA1i problem. program has issues due to references/pointers. * update gitignore * add factorial and binomial coefficient utility functions * update recursive backtracking method to use goroutines and channels * remove main.go (now chapter01.go) * add a makefile * go fmt uses tabs, not spaces * update tests to add todos, add ba1i test file * add count and visit hamming neighbors to rosalind * add ba1i data frequent_words_mismatch.txt to data/ * fix ba1 part i - recursion now uses a map, solving reference problem and obviating channel. * add ba1i problem solved * add BA1j solution and tests * clean up chapter 01 * add ba1j problem test data * clean up BA 1 i tests * clean up and make consistent most frequent kmer methods * add k, l, m to rosalind.go * add pattern to number data * add BA1M number to pattern data * add solution and test for BA1L * add frequency array method * add solutions and tests for BA 1K, 1L, 1M * add 1k, 1l, 1m data sets * add BA1N solution and test * add small fix to ba1n	6 years ago
Charles Reid	e65a3d6726	Add solutions for Chapter 1 (#1 ) * restructure ba1a.go problem - include BA1A() and BA1ADescription() * add a test for problem BA1A * add problem ba1b test * add problem ba1b * add main method * add todo doc * add readme * add Go gitignore * update update function names and docstrings in BA1B * add BA1C (in progress) and initial test of DNA2Bitmask method * complete DNA-bitmask conversion functions * add code to BA1A test to load test case from file * run a simple test in the BA1C() method * add BA1D test problems * add a few more tests * add BA1B test from file * add data directory with text files containing sample data * fill in remaining tests * add BA1E. restructure everyone to use rosalind.go community function file * add matrix of tests for clump finding - problem BA1E * add BA1F solution and functionsa * update tests, BA1F working * add BA1G solution * move chapter 1 problems to folder * add chapter 1 readme * add file i/o functions * update filename * update top level readme with organization info * update import statements and fix compilation errors * fix print statement * add tests from external file for BA1D * add int slice comparison function * add actual rosalind.info inputs (i.e., inputs with no outputs) * update all drivers to properly work. 2018-12-16: completed/submitted correct answers for all chapter 1 problems on rosalind.info. * add BA1H solution and fixes for everybody * ba1h utility function comment	6 years ago
		`@ -0,0 +1,2 @@`
							CAGTGTAAGTAACGGATTGAGGACGTAACGGACTAGTATTCGAGGACAGTGTAATTGAGGACGTAACGGAGTAACGGATCGAGGACTAGTATCAGTGTAATTGAGGACGTAACGGAGTAACGGACAGTGTAACAGTGTAACTAGTATGTAACGGACAGTGTAAGTAACGGAGTAACGGAGTAACGGATCGAGGATTGAGGACCTAGTATCTAGTATTCGAGGATCGAGGATTGAGGACCTAGTATCTAGTATGTAACGGATTGAGGACTTGAGGACCTAGTATTCGAGGATCGAGGAGTAACGGACAGTGTAACAGTGTAATCGAGGATCGAGGACAGTGTAATTGAGGACTCGAGGACTAGTATTTGAGGACTCGAGGATTGAGGACGTAACGGAGTAACGGATCGAGGACTAGTATGTAACGGAGTAACGGACAGTGTAACTAGTATTTGAGGACCAGTGTAACAGTGTAACAGTGTAACAGTGTAACAGTGTAACTAGTATGTAACGGAGTAACGGATTGAGGACGTAACGGAGTAACGGATCGAGGATTGAGGACCTAGTATTTGAGGACGTAACGGATTGAGGACCTAGTATCTAGTATCAGTGTAACTAGTATGTAACGGATCGAGGATCGAGGACAGTGTAATTGAGGACTTGAGGACCAGTGTAATCGAGGATTGAGGACTTGAGGACTTGAGGACTCGAGGACAGTGTAAGTAACGGAGTAACGGATCGAGGACAGTGTAATTGAGGACCTAGTATTTGAGGACCTAGTATGTAACGGATTGAGGACCAGTGTAACTAGTATCTAGTATCTAGTATCAGTGTAATTGAGGACTCGAGGATTGAGGAC
							`6 2`
		`@ -0,0 +1,2 @@`
							TTACTCGCTGGCAGGTTGACGGAGAAATATTGGTGACGGAGAAGACGGAGAATGGGCATATATTGGTTGGCAGGTTTGGGCATTTACTCGCGACGGAGAATTACTCGCTGGGCATTTACTCGCTGGGCATTTACTCGCTGGCAGGTTTGGCAGGTTATATTGGTATATTGGTATATTGGTTGGGCATTTACTCGCGACGGAGAATGGCAGGTTGACGGAGAAGACGGAGAAATATTGGTTTACTCGCATATTGGTGACGGAGAAATATTGGTTTACTCGCTTACTCGCTGGGCATTGGGCATTGGCAGGTTGACGGAGAAGACGGAGAATTACTCGCATATTGGTTTACTCGCGACGGAGAATTACTCGCATATTGGTGACGGAGAAGACGGAGAATTACTCGCTGGCAGGTTTGGGCATTGGGCATTTACTCGCTGGCAGGTTTGGGCATTGGCAGGTTGACGGAGAAGACGGAGAATGGCAGGTTTGGCAGGTTTGGCAGGTTTGGCAGGTTTGGGCATGACGGAGAATTACTCGCTGGCAGGTTTTACTCGCTGGCAGGTTTTACTCGCATATTGGTTGGCAGGTTTTACTCGCTTACTCGCTTACTCGCGACGGAGAAGACGGAGAAATATTGGTATATTGGTATATTGGTTGGCAGGTTTGGCAGGTTTGGCAGGTTATATTGGTTTACTCGCTTACTCGCATATTGGTTGGCAGGTTTGGGCATTGGCAGGTTTGGCAGGTTGACGGAGAATGGCAGGTTGACGGAGAAGACGGAGAATGGGCATTGGGCATGACGGAGAATGGCAGGTT
							`5 3`
		`@ -0,0 +1,2 @@`
							CAATGAGTGATATTGTTTGGTAGCAATCCATAGTTGAGGCCCTACGGAAGTTGCATCCGGGGCCCGTAGGACTCGCGGGCAAAAGATTGCTAAGCATTCTTGGTCACCATCGCAGTATTGCTCGTAGTCGGGTGGGTTTGCCGAACTGATAATGTGCCAGTCCCCGCGGAACCGGAATCAGGGCAACGGCTAGAGATACTCTCCGTGGGTCCTAAGTAGGAGGCTTGGGGCTGAGTGAGCAACCACTTACTCGAGTGTGTTGTTTTCTGTGCGTCCCCCGGGCGGTGTTCATTTAAGGATGACCGGGTGAGTAACCGAACAATTTTGTTGCCATGAAACGCGGCAATAACTCAATCTACCAGTACGGACAAATATAATGTTGGGCCCTTTTAGCTTAACGGACGTCGTCCCATTCTGACCTTAACTAAGACTATAAGGTAGGGGGTCAGATACGACACGGTCAGTAGGTGGATATACCGTGACAAATACCGGCACCTATGCTAATTGCGATTTGGAATGGAACGCGCCGAATACTTCGGATCATATCACCGTCCCTGTACTCGAAAGTTCTGCCACGAACAAGTCTCCTACTTGTGTCTTTTCTCACTGCGAAG
							`5`
		`@ -0,0 +1,2 @@`
							`50`
							GGGGGAAACTTACGGAGTACAAGAAGACCCGGCACAAAGAGAAAACACGTTGCTCGTTAGCTTAAGTTAAGACGTATCGGATATCTATCGTATCCTCGTAGTATTGCTAGCCACTTCACTGGACCAGGCTTACGTATTAGCCTTATGACCCCATTTCGTCTCCGCTGCTACAGCTGTGGAGTTGACGCGTCCGGTGGGCCCTCCGTTAGCAGGTCAGCTCATATTTTCGGCAAGAAATTACCCGGAACGGACCGAAAATGGGGTACAACATGCCCACCCACAACTTAGTACACAACGCTCAGCAAGTAGCTAACGACCGCTGCCGTCGTCAGTATTAGACGCACTTAACCGTACGGAATCCGTGAGTCCTGTTTCCGCCGATCGAATTACGCGCCCGGGTCGTGGGTCCAAAGGTGGCCGATCTCACGTACTGGTGAGTCGCGCGGTCACTTGGCTGTGAGGTCCACCGGCGGCCACAGTAATCTCTGGTGCACCCAGAATCGAGTCTGGATTGTGCACAAAGCTGCCCGCCTCTATTTCTCGGACCTGGCAGAACGCAACGGATGGGTTGAAGATTGGGCCGGTTCCGATGCCCCAAAGTACCCACATTTACTAGGGTGAGGCTGTTCTTTTGAGAGTAGAGACGAAAGCACCCCGACGTAACTGCTGCACACGGGGCTGCTCGGGATACTGTGCCGGAACTAGCGAGGCTCTACCCTCATCGGAAACCAGGCCTCATAATTCTTACAGCGTACTGTGTACTCCACAAGGAGCTGACCAGACATTCCACGTCCATGGATTCGGCTCATGCATACCTCCCGATCCACTCCTGAGCACATTGGATGGACACTTGAACGATGTCCTTAGCGCACGAGACATCAATTCGTGACGGTAGATTGCTCTCACCCTGATGCGGGTAAGTCACGTATTACCCGGCGTGCGGTATGTAGTAATACAGCTATCTACAACAAATGCAACCCGGCAGGTCTCCCATAGACCA
		`@ -0,0 +1,4 @@`
							`# rosalind go package`

							This directory contains the `rosalind` Go package.
+Input
+Output
+CCATGGC