Exemple #1
0
// writeFlankSeqs writes fasta files containing the sequence of unmapped flanks
// identified in the primary hits provided. cutoff specifies the minimum sequence
// length to consider. left and right specify the filenames for the left and right
// flank fasta sequence files.
func writeFlankSeqs(reads string, hits hitSet, cutoff int, left, right string) error {
	f, err := os.Open(reads)
	if err != nil {
		return err
	}
	defer f.Close()

	lf, err := os.Create(left)
	if err != nil {
		return err
	}
	rf, err := os.Create(right)
	if err != nil {
		return err
	}

	r := fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNA))
	sc := seqio.NewScanner(r)
	for sc.Next() {
		seq := sc.Seq().(*linear.Seq)
		h, ok := hits[seq.Name()]
		if !ok {
			continue
		}

		all := seq.Seq
		if h.qStart >= cutoff {
			seq.Seq = all[:h.qStart]
			_, err := fmt.Fprintf(lf, "%60a\n", seq)
			if err != nil {
				return err
			}
		}
		if h.qLen-h.qEnd >= cutoff {
			seq.Seq = all[h.qEnd:]
			_, err := fmt.Fprintf(rf, "%60a\n", seq)
			if err != nil {
				return err
			}
		}
	}
	err = sc.Error()
	if err != nil {
		return err
	}
	err = lf.Close()
	if err != nil {
		return err
	}
	return rf.Close()
}
Exemple #2
0
func main() {
	flag.Parse()
	if *in == "" || *typ < 0 || 2 < *typ {
		flag.Usage()
		os.Exit(1)
	}

	cfn := []func(s seq.Sequence, start, end int) (float64, error){
		0: complexity.WF,
		1: complexity.Entropic,
		2: complexity.Z,
	}[*typ]

	f, err := os.Open(*in)
	if err != nil {
		log.Fatalf("failed to open %q: %v", *in, err)
	}
	defer f.Close()

	sc := seqio.NewScanner(fasta.NewReader(f, linear.NewSeq("", nil, alphabet.DNAgapped)))
	for sc.Next() {
		seq := sc.Seq().(*linear.Seq)

		// err is always nil for a linear.Seq Start() and End().
		c, _ := cfn(seq, seq.Start(), seq.End())

		if *dist {
			fmt.Printf("%s\t%v\t%d\n", seq.Name(), c, seq.Len())
			continue
		}
		if c >= *thresh {
			fmt.Printf("%60a\n", seq)
		}
	}
	if err := sc.Error(); err != nil {
		log.Fatalf("error during fasta read: %v", err)
	}
}