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//go:build ignore
// +build ignore
package main
import (
"fmt"
"io"
"io/ioutil"
"log"
"os"
"strconv"
"strings"
"github.com/biogo/biogo/alphabet"
)
var matrices = []struct {
file string
alpha alphabet.Alphabet
}{
{"NUC.4", alphabet.DNA},
{"NUC.4.4", alphabet.DNAredundant},
{"DAYHOFF", alphabet.Protein},
{"GONNET", alphabet.Protein},
{"IDENTITY", alphabet.Protein},
{"MATCH", alphabet.Protein},
{"BLOSUM100", alphabet.Protein},
{"BLOSUM30", alphabet.Protein},
{"BLOSUM35", alphabet.Protein},
{"BLOSUM40", alphabet.Protein},
{"BLOSUM45", alphabet.Protein},
{"BLOSUM50", alphabet.Protein},
{"BLOSUM55", alphabet.Protein},
{"BLOSUM60", alphabet.Protein},
{"BLOSUM62", alphabet.Protein},
{"BLOSUM65", alphabet.Protein},
{"BLOSUM70", alphabet.Protein},
{"BLOSUM75", alphabet.Protein},
{"BLOSUM80", alphabet.Protein},
{"BLOSUM85", alphabet.Protein},
{"BLOSUM90", alphabet.Protein},
{"BLOSUMN", alphabet.Protein},
{"PAM10", alphabet.Protein},
{"PAM100", alphabet.Protein},
{"PAM110", alphabet.Protein},
{"PAM120", alphabet.Protein},
{"PAM120.cdi", alphabet.Protein},
{"PAM130", alphabet.Protein},
{"PAM140", alphabet.Protein},
{"PAM150", alphabet.Protein},
{"PAM160", alphabet.Protein},
{"PAM160.cdi", alphabet.Protein},
{"PAM170", alphabet.Protein},
{"PAM180", alphabet.Protein},
{"PAM190", alphabet.Protein},
{"PAM20", alphabet.Protein},
{"PAM200", alphabet.Protein},
{"PAM200.cdi", alphabet.Protein},
{"PAM210", alphabet.Protein},
{"PAM220", alphabet.Protein},
{"PAM230", alphabet.Protein},
{"PAM240", alphabet.Protein},
{"PAM250", alphabet.Protein},
{"PAM250.cdi", alphabet.Protein},
{"PAM260", alphabet.Protein},
{"PAM270", alphabet.Protein},
{"PAM280", alphabet.Protein},
{"PAM290", alphabet.Protein},
{"PAM30", alphabet.Protein},
{"PAM300", alphabet.Protein},
{"PAM310", alphabet.Protein},
{"PAM320", alphabet.Protein},
{"PAM330", alphabet.Protein},
{"PAM340", alphabet.Protein},
{"PAM350", alphabet.Protein},
{"PAM360", alphabet.Protein},
{"PAM370", alphabet.Protein},
{"PAM380", alphabet.Protein},
{"PAM390", alphabet.Protein},
{"PAM40", alphabet.Protein},
{"PAM400", alphabet.Protein},
{"PAM40.cdi", alphabet.Protein},
{"PAM410", alphabet.Protein},
{"PAM420", alphabet.Protein},
{"PAM430", alphabet.Protein},
{"PAM440", alphabet.Protein},
{"PAM450", alphabet.Protein},
{"PAM460", alphabet.Protein},
{"PAM470", alphabet.Protein},
{"PAM480", alphabet.Protein},
{"PAM490", alphabet.Protein},
{"PAM50", alphabet.Protein},
{"PAM500", alphabet.Protein},
{"PAM60", alphabet.Protein},
{"PAM70", alphabet.Protein},
{"PAM80", alphabet.Protein},
{"PAM80.cdi", alphabet.Protein},
{"PAM90", alphabet.Protein},
}
func main() {
fmt.Fprintln(os.Stdout, `// DO NOT EDIT. This file was autogenerated by make.go.
// Copyright ©2013 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package matrix provides a variety of alignment scoring matrices for sequence alignment.
package matrix
// All alignment scoring matrices are organised to allow direct lookup using alphabets
// defined in biogo/alphabet. Gap penalties are set to zero for all matrices and the I/L
// single letter amino acid code, "J", is included but not defined for all the protein
// scoring matrices.
var (`)
for i, m := range matrices {
if i != 0 {
fmt.Fprintln(os.Stdout)
}
err := genCode(os.Stdout, m.file, m.alpha)
if err != nil {
log.Fatalf("Failed to create matrix source for %s: %v", m, err)
}
}
fmt.Println(")")
}
func genCode(w io.Writer, m string, a alphabet.Alphabet) error {
f, err := os.Open(m)
if err != nil {
return err
}
b, err := ioutil.ReadAll(f)
if err != nil {
return err
}
s := string(b)
var (
ind = a.LetterIndex()
ref []string
perm []int
mat [][]int
row int
lastBlank bool
)
for _, l := range strings.Split(s, "\n") {
nsl := noSpace(l)
switch {
case len(l) == 0:
if !lastBlank {
lastBlank = true
fmt.Fprintln(w, "\t//")
}
case l[0] == ' ':
ref = strings.Fields(nsl)
perm = make([]int, a.Len())
for i, l := range ref {
li := ind[l[0]]
if li < 0 {
continue
}
perm[li] = i
}
mat = make([][]int, a.Len())
for j := range mat {
mat[j] = make([]int, a.Len())
}
fallthrough
case l[0] == '#':
lastBlank = false
fmt.Fprintf(w, "\t// %s\n", l)
default:
lastBlank = false
fmt.Fprintf(w, "\t// %s\n", l)
for col, f := range strings.Fields(nsl)[1:] {
mat[ind[ref[row][0]]][ind[ref[col][0]]], err = strconv.Atoi(f)
if err != nil {
return err
}
}
row++
}
}
fmt.Fprintf(w, "\t%s = [][]int{\n\t\t/* ", strings.Replace(m, ".", "_", -1))
for j := range mat {
fmt.Printf("%c ", toUpper(a.Letter(j)))
}
fmt.Fprintln(w, "*/")
for i := range mat {
fmt.Printf("\t\t/* %c */ {", toUpper(a.Letter(i)))
for j, e := range mat[i] {
fmt.Fprint(w, e)
if j < len(mat[i])-1 {
fmt.Print(", ")
}
}
fmt.Fprintln(w, "},")
}
fmt.Fprintln(w, "\t}")
return nil
}
func toUpper(l alphabet.Letter) alphabet.Letter {
if l >= 'a' {
return l &^ ' '
}
return l
}
func noSpace(s string) string {
var b []byte
for i := 0; i < len(s); i++ {
if s[i] == ' ' {
if i > 0 && s[i-1] != ' ' {
b = append(b, ' ')
}
continue
}
b = append(b, s[i])
}
return string(b)
}
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