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writer.go
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writer.go
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package fasta
import (
"bytes"
"github.com/evolbioinfo/goalign/align"
)
const (
FASTA_LINE = 80
)
func min_int(a int, b int) int {
if a < b {
return a
}
return b
}
func WriteAlignment(sb align.SeqBag) string {
var buf bytes.Buffer
sb.IterateChar(func(name string, seq []rune) {
buf.WriteString(">")
buf.WriteString(name)
buf.WriteString("\n")
for i := 0; i < len(seq); i++ {
if i%FASTA_LINE == 0 && i > 0 {
buf.WriteString("\n")
}
buf.WriteRune(seq[i])
}
buf.WriteRune('\n')
})
return buf.String()
}
// Write input alignment as standard fasta sequences
// It removes "-" characters.
func WriteSequences(sb align.SeqBag) string {
var buf bytes.Buffer
sb.IterateChar(func(name string, seq []rune) {
buf.WriteString(">")
buf.WriteString(name)
buf.WriteString("\n")
nbchar := 0
for i := 0; i < len(seq); i++ {
if seq[i] != '-' {
buf.WriteRune(seq[i])
nbchar++
if nbchar == FASTA_LINE {
buf.WriteString("\n")
nbchar = 0
}
}
}
if nbchar != 0 {
buf.WriteString("\n")
}
})
return buf.String()
}