k-nucleotide.go

Documentation: golang.org/x/exp/shootout

     1  //go:build ignore
     2  // +build ignore
     3  
     4  /*
     5  Redistribution and use in source and binary forms, with or without
     6  modification, are permitted provided that the following conditions are met:
     7  
     8      * Redistributions of source code must retain the above copyright
     9      notice, this list of conditions and the following disclaimer.
    10  
    11      * Redistributions in binary form must reproduce the above copyright
    12      notice, this list of conditions and the following disclaimer in the
    13      documentation and/or other materials provided with the distribution.
    14  
    15      * Neither the name of "The Computer Language Benchmarks Game" nor the
    16      name of "The Computer Language Shootout Benchmarks" nor the names of
    17      its contributors may be used to endorse or promote products derived
    18      from this software without specific prior written permission.
    19  
    20  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
    21  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
    22  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
    23  ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
    24  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
    25  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
    26  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
    27  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
    28  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
    29  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
    30  POSSIBILITY OF SUCH DAMAGE.
    31  */
    32  
    33  /* The Computer Language Benchmarks Game
    34   * http://shootout.alioth.debian.org/
    35   *
    36   * contributed by The Go Authors.
    37   */
    38  
    39  package main
    40  
    41  import (
    42  	"bufio"
    43  	"bytes"
    44  	"fmt"
    45  	"io"
    46  	"os"
    47  	"sort"
    48  )
    49  
    50  var in *bufio.Reader
    51  
    52  func count(data string, n int) map[string]int {
    53  	counts := make(map[string]int)
    54  	top := len(data) - n
    55  	for i := 0; i <= top; i++ {
    56  		s := data[i : i+n]
    57  		counts[s]++
    58  	}
    59  	return counts
    60  }
    61  
    62  func countOne(data string, s string) int {
    63  	return count(data, len(s))[s]
    64  }
    65  
    66  type kNuc struct {
    67  	name  string
    68  	count int
    69  }
    70  
    71  type kNucArray []kNuc
    72  
    73  func (kn kNucArray) Len() int      { return len(kn) }
    74  func (kn kNucArray) Swap(i, j int) { kn[i], kn[j] = kn[j], kn[i] }
    75  func (kn kNucArray) Less(i, j int) bool {
    76  	if kn[i].count == kn[j].count {
    77  		return kn[i].name > kn[j].name // sort down
    78  	}
    79  	return kn[i].count > kn[j].count
    80  }
    81  
    82  func sortedArray(m map[string]int) kNucArray {
    83  	kn := make(kNucArray, len(m))
    84  	i := 0
    85  	for k, v := range m {
    86  		kn[i].name = k
    87  		kn[i].count = v
    88  		i++
    89  	}
    90  	sort.Sort(kn)
    91  	return kn
    92  }
    93  
    94  func print(m map[string]int) {
    95  	a := sortedArray(m)
    96  	sum := 0
    97  	for _, kn := range a {
    98  		sum += kn.count
    99  	}
   100  	for _, kn := range a {
   101  		fmt.Printf("%s %.3f\n", kn.name, 100*float64(kn.count)/float64(sum))
   102  	}
   103  }
   104  
   105  func main() {
   106  	in = bufio.NewReader(os.Stdin)
   107  	three := []byte(">THREE ")
   108  	for {
   109  		line, err := in.ReadSlice('\n')
   110  		if err != nil {
   111  			fmt.Fprintln(os.Stderr, "ReadLine err:", err)
   112  			os.Exit(2)
   113  		}
   114  		if line[0] == '>' && bytes.Equal(line[0:len(three)], three) {
   115  			break
   116  		}
   117  	}
   118  	data, err := io.ReadAll(in)
   119  	if err != nil {
   120  		fmt.Fprintln(os.Stderr, "ReadAll err:", err)
   121  		os.Exit(2)
   122  	}
   123  	// delete the newlines and convert to upper case
   124  	j := 0
   125  	for i := 0; i < len(data); i++ {
   126  		if data[i] != '\n' {
   127  			data[j] = data[i] &^ ' ' // upper case
   128  			j++
   129  		}
   130  	}
   131  	str := string(data[0:j])
   132  
   133  	print(count(str, 1))
   134  	fmt.Print("\n")
   135  
   136  	print(count(str, 2))
   137  	fmt.Print("\n")
   138  
   139  	interests := []string{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"}
   140  	for _, s := range interests {
   141  		fmt.Printf("%d %s\n", countOne(str, s), s)
   142  	}
   143  }
   144
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