基本完成
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20c23128ee
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c449b57a80
3 changed files with 39 additions and 19 deletions
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@ -6,5 +6,5 @@ sequence combination tool written in Golang
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```
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```
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parser xxx.fas
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parser xxx.fas
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parser xxx.fas yyy.fas
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parser xxx.fas yyy.fas
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parser -o 123 xxx.fas // todo
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parser -o export.nex xxx.fas yyy.fas
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```
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```
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46
parser.go
46
parser.go
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@ -36,13 +36,13 @@ func main() {
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file_names := flag.Args() // []string{"foo", "bar"}
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file_names := flag.Args() // []string{"foo", "bar"}
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fmt.Println("[ export here ]", *file_export)
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fmt.Println("[ export here ]", *file_export)
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// 遍历文件
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// 遍历文件得到基本数据
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sum_nex := make([]dna, 0, 5)
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sum_nex := make([]dna, 0, 5)
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for k, v := range file_names {
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for k, v := range file_names {
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i, j := fas_parser.Fas_parser(v)
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i, j := fas_parser.Fas_parser(v)
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new_nex := dna{v, i, j}
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new_nex := dna{v, i, j}
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sum_nex = append(sum_nex, new_nex)
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sum_nex = append(sum_nex, new_nex)
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fmt.Println("[ working ]", k+1, v)
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fmt.Println("[ working A ]", k+1, v)
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}
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}
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// 整合若干文件的统计
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// 整合若干文件的统计
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@ -54,29 +54,45 @@ func main() {
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f = sum_charset[k-1].To
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f = sum_charset[k-1].To
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}
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}
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t := f + v.count
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t := f + v.count
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fmt.Println("[ working B ]", n, f, t)
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new_charset := charset{n, f, t}
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new_charset := charset{n, f, t}
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sum_charset = append(sum_charset, new_charset)
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sum_charset = append(sum_charset, new_charset)
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}
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}
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fmt.Println(sum_charset)
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// fmt.Println(sum_charset)
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// dna 的整合
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// dna 的整合
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seq := sum_nex[0].min_dna
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ntax := 0
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ntax := 0 // 待修补
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nchar := sum_charset[len(sum_charset)-1].To
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nchar := sum_charset[len(sum_charset)-1].To
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sum_dna := make(map[string][]string)
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for k, v := range sum_nex {
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for k, v := range sum_nex {
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if k == 0 {
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for k1 := range v.min_dna {
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continue
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_, has := sum_dna[k1]
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if !has {
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sum_dna[k1] = make([]string, len(sum_charset))
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}
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}
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}
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last_count := sum_nex[k-1].count
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ntax = k
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for k1, v1 := range v.min_dna {
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}
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if _, ok := seq[k1]; ok {
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for k, v := range sum_nex {
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seq[k1] = seq[k1] + v1
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for _, v1 := range v.min_dna {
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} else {
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for k2 := range sum_dna {
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seq[k1] = seq[k1] + strings.Repeat("?", last_count)
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if _, ok := v.min_dna[k2]; ok {
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sum_dna[k2][k] = v1
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} else {
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sum_dna[k2][k] = strings.Repeat("?", v.count)
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}
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}
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}
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}
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}
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}
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}
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last_data := tmpl_data{ntax, nchar, seq, sum_charset}
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// fmt.Println(sum_dna)
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matrix := make(map[string]string, ntax)
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for k := range sum_dna {
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matrix[k] = strings.Join(sum_dna[k], "")
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}
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// 准备发射到模板的数据
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last_data := tmpl_data{ntax, nchar, matrix, sum_charset}
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// fmt.Println(last_data)
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// fmt.Println(last_data)
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// 读取模板
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// 读取模板
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@ -96,7 +112,7 @@ func main() {
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// 写入 nex 模板
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// 写入 nex 模板
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err = nex_tmpl.Execute(new_file, last_data)
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err = nex_tmpl.Execute(new_file, last_data)
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if err!= nil {
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if err != nil {
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fmt.Println("[ err at tmpl exec ]", err)
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fmt.Println("[ err at tmpl exec ]", err)
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return
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return
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}
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}
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@ -4,13 +4,17 @@ const Nex_tmpl = `#NEXUS
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BEGIN DATA;
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BEGIN DATA;
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DIMENSIONS NTAX={{ .Ntax }} NCHAR={{ .Nchar }};
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DIMENSIONS NTAX={{ .Ntax }} NCHAR={{ .Nchar }};
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FORMAT DATATYPE=DNA GAP=- MISSING=? ; #DATATYPE={}
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FORMAT DATATYPE=DNA GAP=- MISSING=? ; #DATATYPE={}
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MATRIX{{ range $k, $v := .Matrix }}
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MATRIX
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{{- range $k, $v := .Matrix }}
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'{{ $k }}' {{ $v }}{{ end }}
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'{{ $k }}' {{ $v }}{{ end }}
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;
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;
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END;
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END;
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BEGIN SETS;{{ range $_, $i := .Charset }}
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BEGIN SETS;
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CHARSET {{ .Name }} = {{ .From }}-{{ .To }};{{ end }}
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{{- range $_, $i := .Charset }}
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CHARSET {{ $i.Name }} = {{ $i.From }}-{{ $i.To }};
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{{- end }}
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END;
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END;
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`
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`
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// 最后那个 $i 好像有问题
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// 最后那个 $i 好像有问题
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// {{/* $k| printf "%-40s" */}}
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