RegionsToFasta.java

package org.seqcode.tools.sequence;

import java.io.*;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;

import org.seqcode.data.io.FASTAWriter;
import org.seqcode.genome.Genome;
import org.seqcode.genome.Species;
import org.seqcode.genome.location.NamedStrandedRegion;
import org.seqcode.genome.location.Region;
import org.seqcode.genome.location.StrandedRegion;
import org.seqcode.gsebricks.verbs.location.RegionParser;
import org.seqcode.gseutils.Args;
import org.seqcode.gseutils.Pair;


/**
 *  reads a list of regions (one per line) on STDIN.
    Produces on stdout a fasta file containing those regions.
    The genome is specified on the command line as
    --species "Mus musculus;mm8"
*/

public class RegionsToFasta {

    public static void main(String args[]) {
        try {
        	String outfile = Args.parseString(args, "outfile", "");
        	String infile = Args.parseString(args, "infile", "");
            Pair<Species,Genome> pair = Args.parseGenome(args);
            Species organism = pair.car();
            Genome genome = pair.cdr();
            FASTAWriter writer;
            if (!outfile.equals("")) {
            	writer = new FASTAWriter(new PrintStream(outfile));
            } else {
            	writer = new FASTAWriter(System.out);
            }
            writer.useCache(Args.parseFlags(args).contains("cache"));
            int expand = Args.parseInteger(args,"expand",0);
            DateFormat dfm = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
            int count = 0;
            String line;
            BufferedReader reader;
            if (!infile.equals("")) {
            	reader = new BufferedReader(new FileReader(infile));
            } else {
            	reader = new BufferedReader(new InputStreamReader(System.in));
            }
            while ((line = reader.readLine()) != null) {
                line = line.trim();
                StrandedRegion sr = StrandedRegion.fromString(genome, line);
                if (sr != null) {
                    String pieces[] = line.split("\\t");
                    if (pieces.length > 1) {
                        sr = new NamedStrandedRegion(sr, pieces[1], sr.getStrand());
                    }
                    writer.consume(sr.expand(expand,expand));
                } else {
                    Region r = Region.fromString(genome,line);
                    writer.consume(r.expand(expand,expand));   
                }
                count++;
                if (count % 100 == 0) {
                	System.err.println(count+" "+dfm.format(new Date()));
                }
            }


        } catch (Exception e) {
            e.printStackTrace();
        }

    }

}