暂时修好了
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qaqland
parent
e53203768f
commit
c0c60ce5a7
6 changed files with 28 additions and 25 deletions
15
a.nex
15
a.nex
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@ -1,15 +1,16 @@
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#NEXUS
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BEGIN DATA;
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DIMENSIONS NTAX=4 NCHAR=6;
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DIMENSIONS NTAX=4 NCHAR=2031;
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FORMAT DATATYPE=DNA GAP=- MISSING=?;
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MATRIX
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'>Bradybaena circulus circulus' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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'>Bradybaena phaeogramma phaeogramma' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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'>Bradybaena similaris' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------???
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'>Bradybaena virgo virgo' ???tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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'Bradybaena circulus circulus' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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'Bradybaena phaeogramma phaeogramma' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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'Bradybaena similaris' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aactatatg-gtatcatatatagctatttctgctcaatg-taatataaatagccgcagtactctgactgtgctaaggtagcataatcatttggcttataattgaagtctagtatgaaagaagatatgggagttaactgtttcctaaacgtttacttaatttacttagggggtgaaaatacccccacaaacataatagacgagaagacccttgaaatttttagtata---attttaaatcgtgctttttgttggggcgacaaggtagcatagtaaacctactaagtggttttattagaacaaaattgtatgaataattaaattactcaagggataacagcataatattttaaagtttgtgacctcgatgttggactaggacaatatagtttaaaagactattatttttgctctgttcg---------------------????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
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'Bradybaena virgo virgo' ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------tatatattatttggtgtttggtgtgggatagttggtacaggtttaagattattgattcgaatagagttaggtagttctggtgttatagcagaagagcatttctacaatgttattgtaacagctcatgcttttgtaataattttttttatagttatgccaatcatgattggaggttttggaaattgaatagtaccgttgttgattggggcacccgatatgagctttccacgtataaacaatataaggttttgattgttacccccttcttttcttctattaattagaagtagtctagtagaaggcggtgcagggaccggttgaacagtgtatcctccacttagctcacttgtaggtcataggagagctgccgtagacttagcaatcttttctcttcatttggctgggatatcatcaattttaggtgcaatcaattttattacaactatttttaatatacgagccccaggaataactatggaacgtgttagactgtttgtttgatctattttagtgacagtgtttcttttattact-----------------------------------------------------------------------------
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;
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END;
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BEGIN SETS;
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CHARSET ./data/16S.fas = 1-3;
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CHARSET ./data/CO1.fas = 4-6;
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CHARSET ./data/16S.fas = 1-811;
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CHARSET ./data/CO1.fas = 812-1421;
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CHARSET ./data/CO1.mega.fas = 1422-2031;
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END;
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5
count.go
5
count.go
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@ -19,9 +19,8 @@ func fas_sum() []dna {
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}
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// 整合若干文件的统计
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func fas_count() []charset {
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func fas_count(sum_nex []dna) []charset {
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fas_charset := []charset{}
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sum_nex := fas_sum()
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for k, v := range sum_nex {
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n := v.name
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f := 1
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@ -33,6 +32,6 @@ func fas_count() []charset {
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new_charset := charset{n, f, t}
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fas_charset = append(fas_charset, new_charset)
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}
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// fmt.Println(sum_charset)
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fmt.Println(fas_charset)
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return fas_charset
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}
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@ -17,9 +17,9 @@ func main() {
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sum_nex := fas_sum()
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sum_charset := fas_count()
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sum_charset := fas_count(sum_nex)
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sum_dna, ntax, nchar := dna_mix(sum_nex, sum_charset)
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sum_dna, ntax, nchar := fas_mix(sum_nex, sum_charset)
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matrix := make(map[string]string, ntax)
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for k := range sum_dna {
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9
mix.go
9
mix.go
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@ -2,13 +2,13 @@ package main
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import "strings"
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func dna_mix(sum_nex []dna, sum_charset []charset) (map[string][]string, int, int) {
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func fas_mix(sum_nex []dna, sum_charset []charset) (map[string][]string, int, int) {
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// dna 的整合
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ntax := 0
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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 _, v := range sum_nex {
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for k1 := range v.min_dna {
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for k1 := range v.min {
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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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@ -17,12 +17,13 @@ func dna_mix(sum_nex []dna, sum_charset []charset) (map[string][]string, int, in
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}
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}
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for k, v := range sum_nex {
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for _, v1 := range v.min_dna {
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for _, v1 := range v.min {
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for k2 := range sum_dna {
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if _, ok := v.min_dna[k2]; ok {
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if _, ok := v.min[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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// 之前就没写错吗
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}
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}
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}
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3
nex.tmpl
3
nex.tmpl
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@ -4,7 +4,8 @@ BEGIN DATA;
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FORMAT DATATYPE=DNA GAP=- MISSING=?;
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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 }}
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{{- end }}
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;
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END;
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BEGIN SETS;
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13
parser.go
13
parser.go
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@ -3,12 +3,13 @@ package main
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import (
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"fmt"
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"io/ioutil"
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"strings"
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)
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type dna struct {
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name string
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count int
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min_dna map[string]string
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min map[string]string
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}
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// 读取fas文件
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@ -25,24 +26,24 @@ func fas_parser(file_name string) dna {
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i := 0 // acgt行计数
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j := -1 // 标题行计数
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seq := make(map[string]string)
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section := ""
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indid := ""
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for k, v := range f {
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switch v {
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case '>':
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j = k
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count++
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j = k + 1
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case '\n':
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if j != -1 {
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section = string(f[j:k])
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indid = string(f[j:k])
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i = k + 1
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j = -1
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continue
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}
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seq[section] = seq[section] + string(f[i:k])
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seq[indid] = seq[indid] + strings.ToLower(string(f[i:k]))
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i = k + 1
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}
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}
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count = len(seq[indid])
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// for k1, v1 := range seq {
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// fmt.Println(k1)
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// fmt.Println(v1)
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