intersect.org

package main
import (
	  //<<Imports>>
)
func main(){
	  //<<Main function>>
}

//<<Declare options>>
//<<Set usage>>
//<<Parse options>>
//<<Run \texttt{Intersect}>>
//<<Print the results>>

optR := flag.String("r", "", "reference sequence")

optP := flag.Float64("p", 0.975,
	  "threshold p-value for a shustring length")

optN := flag.Bool("n", false, "print segregating sites (Ns) " +
	  "in the output sequences")

optF := flag.Float64("f", 1.0,
	  "intersection sensitivity threshold")

optT := flag.Int("t", 1, "number of threads")

"flag"

u := "intersect [option]..."
p := "Find common homologous regions in a set of genomes"
e := "intersect -r subject.fna query1.fna query2.fna ..."
clio.Usage(u, p, e)

"github.com/evolbioinf/clio"

flag.Parse()
//<<Check the reference>>
//<<Read reference's contigs>>
//<<Set parameters>>

"fmt"
"os"

if *optR == "" {
	  fmt.Fprintf(os.Stderr,
		  "please specify the reference sequence\n")
	  os.Exit(1)
}

f, _ := os.Open(*optR)
referenceContigs := fastautils.ReadAll(f)
f.Close()

"github.com/ivantsers/fastautils"

//<<Interpret *optP>>
//<<Interpret *optF>>
//<<Create a Parameters struct>>

if *optP > 1 || *optP < 0 {
	  fmt.Fprintf(os.Stderr,
		  "can't use %v as a sensitivity threshold\n",
		  *optF)
	  os.Exit(1)
}

if *optF > 1.0 || *optF <= 0.0 {
	  fmt.Fprintf(os.Stderr,
		  "can't use %v as a sensitivity threshold, " +
			  "please use a value in the interval (0,1]",
		  *optF)
	  os.Exit(1)
}

parameters := chr.Parameters{
	  Reference:       referenceContigs,
	  QueryPaths:      flag.Args(),
	  Threshold:       *optF,
	  ShustrPval:      *optP,
	  PrintN:          *optN,
	  NumThreads:      *optT,
}

"github.com/ivantsers/chr"

isc := chr.Intersect(parameters)

for _, seq := range(isc) {
	  fmt.Fprintf(os.Stdout, "%s\n", seq)
}