Merge pull request #1 from MalacoLab/rebuild

Rebuild

.gitignore

@@ -0,0 +1,2 @@
+a.nex
+test.go

a.nex

@@ -0,0 +1,16 @@
+#NEXUS
+BEGIN DATA;
+	DIMENSIONS NTAX=4 NCHAR=2031;
+	FORMAT DATATYPE=DNA GAP=- MISSING=?;
+MATRIX
+'Bradybaena circulus circulus' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
+'Bradybaena phaeogramma phaeogramma' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
+'Bradybaena similaris' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+'Bradybaena virgo virgo' ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
+;
+END;
+BEGIN SETS;
+	CHARSET ./data/16S.fas = 1-811;
+	CHARSET ./data/CO1.fas = 812-1421;
+	CHARSET ./data/CO1.mega.fas = 1422-2031;
+END;

count.go

@@ -0,0 +1,49 @@
+package main
+
+import (
+	"fmt"
+	"regexp"
+)
+
+type charset struct {
+	Name string
+	From int
+	To   int
+}
+
+// 遍历文件得到基本数据
+func fas_sum() []dna {
+	sum := []dna{}
+	for i, f := range file_input {
+		sum = append(sum, fas_parser(f))
+		fmt.Println("[ working A ]", i+1, f)
+	}
+	return sum
+}
+
+// 整合若干文件的统计
+func fas_count(sum_nex []dna) []charset {
+	fas_charset := []charset{}
+	for k, v := range sum_nex {
+		n := fas_name(v.name)
+		f := 1
+		if k != 0 {
+			f = fas_charset[k-1].To + 1
+		}
+		t := f + v.count - 1
+		fmt.Println("[ working B ]", n, f, t)
+		new_charset := charset{n, f, t}
+		fas_charset = append(fas_charset, new_charset)
+	}
+	fmt.Println(fas_charset)
+	return fas_charset
+}
+
+func fas_name(old_name string) string {
+	//needed to import string
+	compileRegex := regexp.MustCompile(`(\w+)\.\w+`)
+	matchArr := compileRegex.FindStringSubmatch(old_name)
+	//needed to use the string get from the old string
+	new_name := matchArr[len(matchArr)-1]
+	return new_name
+}

flag.go

@@ -0,0 +1,20 @@
+package main
+
+import (
+	"flag"
+	"fmt"
+)
+
+var (
+	file_output string
+	file_input  []string
+)
+
+func dna_flag() {
+	flag.StringVar(&file_output, "o", "a.nex", "files name wait to out")
+	flag.Parse()
+	file_input = flag.Args() // []string{"foo", "bar"}
+	fmt.Println("==============")
+	fmt.Println("[input  file:]", file_input)
+	fmt.Println("[output file:]", file_output)
+}

gocomb.go

@@ -0,0 +1,33 @@
+package main
+
+import (
+	"strings"
+)
+
+type tmpl_data struct {
+	Ntax    int
+	Nchar   int
+	Matrix  map[string]string
+	Charset []charset
+}
+
+func main() {
+
+	dna_flag()
+
+	sum_nex := fas_sum()
+
+	sum_charset := fas_count(sum_nex)
+
+	sum_dna, ntax, nchar := fas_mix(sum_nex, sum_charset)
+
+	matrix := make(map[string]string, ntax)
+	for k := range sum_dna {
+		matrix[k] = strings.Join(sum_dna[k], "")
+	}
+
+	// 准备发射到模板的数据
+	last_data := tmpl_data{ntax, nchar, matrix, sum_charset}
+	// fmt.Println(last_data)
+	do_impl(last_data)
+}

mix.go

@@ -0,0 +1,33 @@
+package main
+
+import "strings"
+
+func fas_mix(sum_nex []dna, sum_charset []charset) (map[string][]string, int, int) {
+	// dna 的整合
+	ntax := 0
+	nchar := sum_charset[len(sum_charset)-1].To
+	sum_dna := make(map[string][]string)
+	for _, v := range sum_nex {
+		for k1 := range v.min {
+			_, has := sum_dna[k1]
+			if !has {
+				sum_dna[k1] = make([]string, len(sum_charset))
+				ntax++
+			}
+		}
+	}
+	for k, v := range sum_nex {
+		for _, v1 := range v.min {
+			for k2 := range sum_dna {
+				if _, ok := v.min[k2]; ok {
+					sum_dna[k2][k] = v1
+				} else {
+					sum_dna[k2][k] = strings.Repeat("?", v.count)
+					// 之前就没写错吗
+				}
+			}
+		}
+	}
+	// fmt.Println(sum_dna)
+	return sum_dna, ntax, nchar
+}

nex.tmpl

@@ -1,12 +1,11 @@
-package fas_parser
+#NEXUS
-
-const Nex_tmpl = `#NEXUS
 BEGIN DATA;
 	DIMENSIONS NTAX={{ .Ntax }} NCHAR={{ .Nchar }};
 	FORMAT DATATYPE=DNA GAP=- MISSING=?;
 MATRIX
 {{- range $k, $v := .Matrix }}
-'{{ $k }}' {{ $v }}{{ end }}
+'{{ $k }}' {{ $v }}
+{{- end }}
 ;
 END;
 BEGIN SETS;
@@ -14,7 +13,3 @@ BEGIN SETS;
 	CHARSET {{ $i.Name }} = {{ $i.From }}-{{ $i.To }};
 {{- end }}
 END;
-`
-
-// 最后那个 $i 好像有问题
-// {{/* $k| printf "%-40s" */}}

parser.go

@@ -1,119 +1,53 @@
 package main
 
 import (
-	"flag"
 	"fmt"
-	fas_parser "gocomb/src"
+	"io/ioutil"
-	"os"
 	"strings"
-	"text/template"
 )
 
 type dna struct {
 	name  string
-	min_dna map[string]string
 	count int
+	min   map[string]string
 }
 
-type charset struct {
+// 读取fas文件
-	Name string
+func fas_parser(file_name string) dna {
-	From int
-	To   int
-}
 
-type tmpl_data struct {
+	// 读取文件
-	Ntax    int
+	f, err := ioutil.ReadFile("./" + file_name)
-	Nchar   int
-	Matrix  map[string]string
-	Charset []charset
-}
-
-func main() {
-
-	// 读取命令行，这里一定要是指针
-	file_export := flag.String("o", "a.nex", "files name wait to out")
-	flag.Parse()
-	file_names := flag.Args() // []string{"foo", "bar"}
-	fmt.Println("[ export here ]", *file_export)
-
-	// 遍历文件得到基本数据
-	sum_nex := make([]dna, 0, 5)
-	for k, v := range file_names {
-		i, j := fas_parser.Fas_parser(v)
-		new_nex := dna{v, i, j}
-		sum_nex = append(sum_nex, new_nex)
-		fmt.Println("[ working A ]", k+1, v)
-	}
-
-	// 整合若干文件的统计
-	sum_charset := []charset{}
-	for k, v := range sum_nex {
-		n := v.name
-		f := 1
-		if k != 0 {
-			f = sum_charset[k-1].To + 1
-		}
-		t := f + v.count - 1
-		fmt.Println("[ working B ]", n, f, t)
-		new_charset := charset{n, f, t}
-		sum_charset = append(sum_charset, new_charset)
-	}
-	// fmt.Println(sum_charset)
-
-	// dna 的整合
-	ntax := 0
-	nchar := sum_charset[len(sum_charset)-1].To
-	sum_dna := make(map[string][]string)
-	for _, v := range sum_nex {
-		for k1 := range v.min_dna {
-			_, has := sum_dna[k1]
-			if !has {
-				sum_dna[k1] = make([]string, len(sum_charset))
-				ntax ++
-			}
-		}
-	}
-	for k, v := range sum_nex {
-		for _, v1 := range v.min_dna {
-			for k2 := range sum_dna {
-				if _, ok := v.min_dna[k2]; ok {
-					sum_dna[k2][k] = v1
-				} else {
-					sum_dna[k2][k] = strings.Repeat("?", v.count)
-				}
-			}
-		}
-	}
-	// fmt.Println(sum_dna)
-
-	matrix := make(map[string]string, ntax)
-	for k := range sum_dna {
-		matrix[k] = strings.Join(sum_dna[k], "")
-	}
-
-	// 准备发射到模板的数据
-	last_data := tmpl_data{ntax, nchar, matrix, sum_charset}
-	// fmt.Println(last_data)
-
-	// 读取模板
-	nex_tmpl, err := template.New("nex").Parse(fas_parser.Nex_tmpl)
 	if err != nil {
-		fmt.Println("[ tmpl err ]", err)
+		fmt.Println(err)
-		return
+		return dna{"", 0, nil}
 	}
 
-	// 覆盖创建要写入的 nex 文件
+	count := 0
-	new_file, err := os.OpenFile(*file_export, os.O_WRONLY|os.O_TRUNC|os.O_CREATE, 0666)
+	i := 0  // acgt行计数
-	if err != nil {
+	j := -1 // 标题行计数
-		fmt.Println("[ create or open file error ]", err)
+	seq := make(map[string]string)
-		return
+	indid := ""
-	}
-	defer new_file.Close()
 
-	// 写入 nex 模板
+	for k, v := range f {
-	err = nex_tmpl.Execute(new_file, last_data)
+		switch v {
-	if err != nil {
+		case '>':
-		fmt.Println("[ err at tmpl exec ]", err)
+			j = k + 1
-		return
+		case '\n':
+			if j != -1 {
+				indid = string(f[j:k])
+				i = k + 1
+				j = -1
+				continue
+			}
+			seq[indid] = seq[indid] + strings.ToLower(string(f[i:k]))
+			i = k + 1
 		}
 	}
+	count = len(seq[indid])
+	// for k1, v1 := range seq {
+	// 	fmt.Println(k1)
+	// 	fmt.Println(v1)
+	// }
+	// fmt.Println(count)
+	return dna{file_name, count, seq}
+}

src/fas_parser.go

@@ -1,53 +0,0 @@
-package fas_parser
-
-import(
-	"io/ioutil"
-	"fmt"
-)
-
-func Fas_parser(file_name string) (map[string]string, int) {
-	f, err := ioutil.ReadFile("./" + file_name)
-	if err != nil {
-		fmt.Println(err)
-		return nil, 0
-	}
-	// fmt.Println(f)
-	count := 0
-	i := 0 // DNA行计数
-	j := 0 // 非序列行计数
-	seq := make(map[string]string)
-	section := ""
-	// fmt.Println('a', 'c', 'g', 't', '-', '\n', '\r')
-	for k, v := range f {
-		switch v {
-		case 'a', 'c', 'g', 't', '-':
-			if j != 0 {
-				continue
-			}
-			if i == 0 {
-				i = k
-			}
-		case '\n':
-			if i != 0 {
-				seq[section] = seq[section] + string(f[i:k])
-				if len(seq) < 2 && j == 0 {
-					count += k - i
-				}
-				i = 0
-				continue
-			}
-			section = string(f[j:k])
-			j = 0
-		default:
-			if j == 0 {
-				j = k + 1
-			}
-		}
-	}
-	// for k1, v1 := range seq {
-	// 	fmt.Println(k1)
-	// 	fmt.Println(v1)
-	// }
-	// fmt.Println(count)
-	return seq, count
-}

tmpl.go

@@ -0,0 +1,39 @@
+package main
+
+import (
+	"fmt"
+	"io/ioutil"
+	"os"
+	"text/template"
+)
+
+func do_impl(last_data tmpl_data) {
+
+	f, err := ioutil.ReadFile("nex.tmpl")
+	if err != nil {
+		fmt.Println(err)
+		return
+	}
+
+	// 读取模板
+	nex_tmpl, err := template.New("nex").Parse(string(f))
+	if err != nil {
+		fmt.Println("[ tmpl err ]", err)
+		return
+	}
+
+	// 覆盖创建要写入的 nex 文件
+	new_file, err := os.OpenFile(file_output, os.O_WRONLY|os.O_TRUNC|os.O_CREATE, 0666)
+	if err != nil {
+		fmt.Println("[ create or open file error ]", err)
+		return
+	}
+	defer new_file.Close()
+
+	// 写入 nex 模板
+	err = nex_tmpl.Execute(new_file, last_data)
+	if err != nil {
+		fmt.Println("[ err at tmpl exec ]", err)
+		return
+	}
+}