11 "github.com/curii/lightning/hgvs"
14 type diffFasta struct{}
16 func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
20 fmt.Fprintf(stderr, "%s\n", err)
23 flags := flag.NewFlagSet("", flag.ContinueOnError)
24 flags.SetOutput(stderr)
25 offset := flags.Int("offset", 0, "coordinate offset")
26 sequence := flags.String("sequence", "chr1", "sequence label")
27 err = flags.Parse(args)
28 if err == flag.ErrHelp {
31 } else if err != nil {
34 if len(flags.Args()) != 2 {
35 err = fmt.Errorf("usage: %s [options] a.fasta b.fasta", prog)
40 errs := make(chan error, 2)
41 for idx, fnm := range flags.Args() {
44 f, err := os.Open(fnm)
50 scanner := bufio.NewScanner(f)
52 buf := scanner.Bytes()
53 if len(buf) > 0 && buf[0] != '>' {
54 fasta[idx] = append(fasta[idx], bytes.ToUpper(buf)...)
60 for range flags.Args() {
61 if err = <-errs; err != nil {
66 variants := hgvs.Diff(string(fasta[0]), string(fasta[1]))
68 for i := range variants {
69 variants[i].Position += *offset
72 for _, v := range variants {
73 fmt.Fprintf(stdout, "%s:g.%s\t%s\t%d\t%s\t%s\n", *sequence, v.String(), *sequence, v.Position, v.Ref, v.New)