/
packseqs.go
52 lines (44 loc) · 1.04 KB
/
packseqs.go
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package main
import (
"crypto/md5"
"fmt"
"github.com/kortschak/BioGo/align/pals"
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"os"
"path/filepath"
)
func packSequence(fileName string) *seq.Seq {
_, name := filepath.Split(fileName)
packer := pals.NewPacker(name)
if file, err := os.Open(fileName); err == nil {
md5hash, _ := util.Hash(md5.New(), file)
logger.Printf("Reading %s: %s", fileName, fmt.Sprintf("%x", md5hash))
seqFile := fasta.NewReader(file)
f, p := logger.Flags(), logger.Prefix()
if verbose {
logger.SetFlags(0)
logger.SetPrefix("")
logger.Println("Sequence \t Length\t Bin Range")
}
var sequence *seq.Seq
for {
if sequence, err = seqFile.Read(); err == nil {
if s := packer.Pack(sequence); verbose {
logger.Println(s)
}
} else {
break
}
}
if verbose {
logger.SetFlags(f)
logger.SetPrefix(p)
}
} else {
logger.Fatalf("Error: %v.\n", err)
}
packer.FinalisePack()
return packer.Packed
}