/
parser.go
61 lines (54 loc) · 1.57 KB
/
parser.go
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package parser
import (
"fmt"
"io"
"os"
"path"
"github.com/biogo/biogo/alphabet"
"github.com/biogo/biogo/io/seqio/fasta"
"github.com/biogo/biogo/seq"
"github.com/biogo/biogo/seq/linear"
"github.com/genoassist/constants"
"github.com/genoassist/replica/components"
"github.com/genoassist/result"
)
// structure of the parser
type prser struct {
filePath string // path of the file the parser will operate on
outPath string // output directory where to store results
assemblerName string // name of the assembler to parse the results of
}
// New creates and returns a new parser struct
func New(fp, op, ap string) (components.Component, error) {
if fp == "" {
return nil, fmt.Errorf("cannot initialize parser with an empty file path")
}
return &prser{
filePath: fp,
outPath: op,
assemblerName: ap,
}, nil
}
// Process performs the work of the parser
func (p *prser) Process() (*result.Result, error) {
outDir := constants.AvailableAssemblers[p.assemblerName].OutputDir
contigsFile := constants.AvailableAssemblers[p.assemblerName].AssemblyFileName
ioRdr, err := os.Open(path.Join(p.outPath, outDir, contigsFile))
if err != nil {
return nil, fmt.Errorf("cannot open file: %v", err)
}
fastaRdr := fasta.NewReader(ioRdr, linear.NewSeq("", nil, alphabet.DNA))
var sequences []seq.Sequence
for {
inSeq, err := fastaRdr.Read()
if err != nil {
if err != io.EOF {
return nil, fmt.Errorf("cannot read sequence: %v", err)
}
break
}
sequences = append(sequences, inSeq)
}
res := result.New(p.assemblerName, sequences)
return res, nil
}