FTPTest.java

package org.genedb.crawl;

import java.io.File;
import java.io.IOException;

import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMRecordIterator;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMFileReader.ValidationStringency;

import org.apache.log4j.Logger;

import uk.ac.sanger.artemis.components.variant.FTPSeekableStream;

import java.net.SocketException;
import java.net.URL;
import java.util.Map;

import junit.framework.TestCase;

public class FTPTest extends TestCase {

	private static final Logger logger = Logger.getLogger(FTPTest.class);

	private static final String[] urls = new String[] {
		//"ftp://ftp.sanger.ac.uk/pub/mouse_genomes/current_bams/129S1.bam",
		//"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA19331/alignment/NA19331.chromX.LS454.ssaha2.LWK.exon_targetted.20100311.bam"
		//"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA19331/alignment/NA19331.chrom20.ILLUMINA.bwa.LWK.low_coverage.20111114.bam"
		//"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA19331/alignment/NA19331.chrom20.ILLUMINA.bwa.LWK.low_coverage.20120522.bam"
		"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00109/alignment/HG00109.unmapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam"
	};

	public void testURLs() throws SocketException, IOException {
		for (String url : urls) {
			run (new URL(url));
		}
	}

	public void run(URL url) throws SocketException, IOException {

		FTPSeekableStream fss = new FTPSeekableStream(url);
		File index = fss.getIndexFile();

		SAMFileReader reader = new SAMFileReader(fss, index, false);
		reader.getFileHeader();

		reader.setValidationStringency(ValidationStringency.SILENT);

		logger.info("attributes");
		for (Map.Entry<String, String> entry : reader.getFileHeader().getAttributes()) {
			logger.info(String.format("%s : %s", entry.getKey(), entry.getValue()));
		}

		logger.info("sequences");
		for (SAMSequenceRecord ssr : reader.getFileHeader().getSequenceDictionary().getSequences()) {
			logger.info(String.format("%s : %s ", ssr.getSequenceName(),  ssr.getSequenceLength() ));
		}

		logger.info("sequences");
		for (SAMSequenceRecord ssr : reader.getFileHeader().getSequenceDictionary().getSequences()) {

//			if (! ssr.getSequenceName().equals("NT_166325")) {
//				continue;
//			}

			int length = ssr.getSequenceLength();

			int min = 100;
			int max = 100000;

			if (min >= length) {
				min = 0;
			}

			//logger.warn((max >= length));

			if (max >= length) {
				max = length;
			}

			if (min >= max) {
				min = 0;
			}

			logger.info(String.format("Sequence: %s (%s) %s-%s", ssr.getSequenceName(), length, min, max));

			SAMRecordIterator i = reader.query(ssr.getSequenceName(), min, max, false);

			while ( i.hasNext() )  {
				SAMRecord record = i.next();
				logger.info(String.format("Read: %s (%s (%s-%s) %s) / %s",
						record.getReadName(),
						min,
						record.getAlignmentStart(),
						record.getAlignmentEnd(),
						max,
						record.getFlags()));

				assertTrue(record.getAlignmentStart() >= min);
			}

			i.close();

			logger.info("_________________________________________________");
		}

		logger.info("Done");

	}











}