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Commit aa30c423 authored by “kpepper”'s avatar “kpepper”
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Fix for RT ticket #642944. ACT can now handle NCBI Blast web site comparison... 

Fix for RT ticket #642944. ACT can now handle NCBI Blast web site comparison files. This is a workaround for the fact that DoubleACT and WebACT are currently down
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src/main/java/uk/ac/sanger/artemis/BlastWebSiteHitTableComparisonData.java 0 → 100644
+ 189
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View file @ aa30c423
/* BlastServerTableComparisonData.java
*
* This file is part of Artemis
*
* Copyright (C) 2018 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.*;
import java.util.List;
import java.util.StringTokenizer;
/**
* This class implements the SimpleComparisonData interface
* for blast web site hit table output.
*
* @author kp11
*/
public class BlastWebSiteHitTableComparisonData extends SimpleComparisonData {
/** Min number of fields in web site blastn/tblastx file. */
public static final int MIN_NUM_FIELDS = 12;
/** Max number of fields in web site blastn/tblastx file. */
public static final int MAX_NUM_FIELDS = 14;
/** Comparison file descriptive type. */
public static final String TYPE = "Blast web site hit table comparison data";
/**
* Create a new BlastWebSiteHitTableComparisonData by reading from the given
* LinePushBackReader.
*/
public BlastWebSiteHitTableComparisonData (final LinePushBackReader stream)
throws IOException {
super (stream);
}
/**
* Create a new, empty instance of BlastServerTableComparisonData.
*/
public BlastWebSiteHitTableComparisonData () {
}
/**
* Returns a new, empty instance of this type of object;
*/
protected SimpleComparisonData getNewSimpleComparisonData () {
return new BlastWebSiteHitTableComparisonData ();
}
/**
* Make an AlignMatch object from the given String.
*/
private static AlignMatch makeMatchFromStringStatic (String line)
throws IOException {
if (line.trim ().length () == 0 || line.startsWith ("#")) {
return null;
}
final StringTokenizer tokenizer = new StringTokenizer (line, "\t");
int numTokens = tokenizer.countTokens ();
if (
numTokens < BlastWebSiteHitTableComparisonData.MIN_NUM_FIELDS ||
numTokens > BlastWebSiteHitTableComparisonData.MAX_NUM_FIELDS) {
final String message = "while reading " +
BlastWebSiteHitTableComparisonData.TYPE +
": unexpected number of fields for this line: " + line;
throw new ComparisonDataParseException (message);
}
// Parse fields from line...
// throw away the query name
tokenizer.nextToken ();
// throw away the subject name
tokenizer.nextToken ();
// % ident
final String percentIdentToken = tokenizer.nextToken ();
// throw away alignment length
tokenizer.nextToken ();
// throw away mismatches
tokenizer.nextToken ();
// throw away gap opens
tokenizer.nextToken ();
// Query start/end
final String qStartToken = tokenizer.nextToken ();
final String qEndToken = tokenizer.nextToken ();
final String sStartToken = tokenizer.nextToken ();
final String sEndToken = tokenizer.nextToken ();
// throw away evalue
tokenizer.nextToken ();
// % bit score
final String scoreToken = tokenizer.nextToken ();
// And ignore all the end fields for tblastx
try {
final int score = (int)(Float.valueOf (scoreToken).floatValue ());
final int percentIdent = (int)(Float.valueOf (percentIdentToken).floatValue ());
final int qStart = Integer.valueOf (qStartToken).intValue ();
final int qEnd = Integer.valueOf (qEndToken).intValue ();
final int sStart = Integer.valueOf (sStartToken).intValue ();
final int sEnd = Integer.valueOf (sEndToken).intValue ();
return makeAlignMatch (sStart, sEnd, qStart, qEnd, score,
percentIdent);
} catch (NumberFormatException e) {
throw new IOException ("while reading " +
BlastWebSiteHitTableComparisonData.TYPE +
": failed to parse a number from this string: " +
e.getMessage ());
}
}
/**
* Make an AlignMatch object from the given String. The String must be in
* a format appropriate for this object.
*/
@Override
protected AlignMatch makeMatchFromString (final String line)
throws IOException {
return makeMatchFromStringStatic (line);
}
/**
* Returns true if and only if the given line is in the correct format for
* this type of ComparisonData. This should be as strict as possible.
*/
public static boolean formatCorrect (final List<String> headers) {
boolean result = false;
if (headers.size() >= 4) {
String blastTypeHeader = headers.get(0);
String iterationHeader = headers.get(1);
String queryHeader = headers.get(2);
String ridHeader = headers.get(3);
if (
(blastTypeHeader.startsWith ("# tblastx") || blastTypeHeader.startsWith ("# blastn")) &&
iterationHeader.startsWith ("# Iteration:") &&
queryHeader.startsWith ("# Query:") &&
ridHeader.startsWith ("# RID:")) {
result = true;
}
}
return result;
}
}
src/main/java/uk/ac/sanger/artemis/ComparisonDataFactory.java
+ 97
− 19
View file @ aa30c423
......@@ -4,7 +4,7 @@
*
* This file is part of Artemis
*
* Copyright (C) 1999-2002 Genome Research Limited
* Copyright (C) 1999-2018 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
......@@ -20,7 +20,6 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ComparisonDataFactory.java,v 1.1 2004-06-09 09:44:16 tjc Exp $
*/
package uk.ac.sanger.artemis;
......@@ -29,6 +28,10 @@ import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.*;
import java.util.LinkedList;
import java.util.List;
import org.apache.log4j.Logger;
/**
* This class contains the method readComparisonData (), which returns an
......@@ -39,47 +42,122 @@ import java.io.*;
**/
public class ComparisonDataFactory {
/** Logging instance. */
private static Logger logger4j = Logger.getLogger(ComparisonDataFactory.class);
/**
* This method creates an appropriate ComparisonData object from a Document.
**/
*/
static public ComparisonData readComparisonData (Document data_document)
throws IOException {
final Reader in_file = data_document.getReader ();
String fileName = data_document.getName();
final LinePushBackReader pushback_reader =
new LinePushBackReader (in_file);
final String line = pushback_reader.readLine ();
if (line == null) {
throw new IOException ("End of file while reading from: " +
data_document);
String line = null;
List<String> headers = null;
try {
line = peekFirstLine(pushback_reader, fileName);
headers = readHeaders(pushback_reader, fileName);
} catch (IOException e) {
try {
// close the reader
pushback_reader.close();
} catch (IOException ioe) {
// Ignore
}
throw e;
}
pushback_reader.pushBack (line);
if (BlastWebSiteHitTableComparisonData.formatCorrect (headers)) {
logger4j.info("Loading Blast web site hit table comparison file: " + fileName);
return new BlastWebSiteHitTableComparisonData (pushback_reader);
}
if (MSPcrunchComparisonData.formatCorrect (line)) {
logger4j.info("Loading crunch comparison file: " + fileName);
return new MSPcrunchComparisonData (pushback_reader);
} else {
if (SSAHAComparisonData.formatCorrect (line)) {
logger4j.info("Loading SSAHA comparison file: " + fileName);
return new SSAHAComparisonData (pushback_reader);
} else {
if (BlastM8ComparisonData.formatCorrect (line)) {
return new BlastM8ComparisonData (pushback_reader);
if (MegaBlastComparisonData.formatCorrect (line)) {
logger4j.info("Loading mega blast comparison file: " + fileName);
return new MegaBlastComparisonData (pushback_reader);
} else {
if (MegaBlastComparisonData.formatCorrect (line)) {
return new MegaBlastComparisonData (pushback_reader);
if (BlastM8ComparisonData.formatCorrect (line)) {
logger4j.info("Loading Blast m8 comparison file: " + fileName);
return new BlastM8ComparisonData (pushback_reader);
} else {
// if (tokenizer.countTokens () < 8) {
// return new MUMmerComparisonData (pushback_reader);
// } else {
throw new IOException ("cannot understand the comparison file format");
// }
try {
// close the reader
pushback_reader.close();
} catch (IOException ioe) {
// Ignore
}
logger4j.info("Failed to load ACT comparison file: " + fileName);
throw new IOException ("cannot understand the comparison file format");
}
}
}
}
}
protected static List<String> readHeaders(LinePushBackReader reader, String fileName) throws IOException {
List<String> headerList = new LinkedList<String>();
String line = null;
boolean finished = false;
do {
line = reader.readLine();
if (line == null) {
throw new IOException (
"End of file while reading from: " +
fileName);
}
if (line.startsWith("#")) {
headerList.add(line);
} else {
finished = true;
}
} while (!finished);
reader.pushBack(line);
return headerList;
}
protected static String peekFirstLine(LinePushBackReader reader, String fileName) throws IOException {
final String line = reader.readLine ();
if (line == null) {
throw new IOException (
"End of file while reading from: " +
fileName);
}
reader.pushBack(line);
return line;
}
}
src/main/java/uk/ac/sanger/artemis/MegaBlastComparisonData.java
+ 0
− 1
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......@@ -29,7 +29,6 @@ import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.*;
import java.util.StringTokenizer;
import java.util.Vector;
/**
* This class implements the ComparisonData interface for MegaBlast output.
......
src/test/java/uk/ac/sanger/artemis/ComparisonDataFactoryTest.java 0 → 100644
+ 506
− 0
View file @ aa30c423
package uk.ac.sanger.artemis;
import static org.junit.Assert.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.util.List;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
import static org.mockito.Mockito.*;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.LinePushBackReader;
/**
* JUnit test for the ComparisonDataFactory
* class and associated functionality.
*
* @author kp11
*
*/
public class ComparisonDataFactoryTest
{
@Mock
Document comparisonDoc;
@Before
public void setUp() throws Exception {
MockitoAnnotations.initMocks(this);
}
/**
* Test the peekFirstLine method.
* @throws Exception
*/
@Test
public void testPeekFirstLine() throws Exception
{
// Test first line retrieval works
String testText = "Line-1\nLine-2\nLine3";
StringReader reader = new StringReader(testText);
LinePushBackReader pushbackReader = new LinePushBackReader(reader);
String line = ComparisonDataFactory.peekFirstLine(pushbackReader, "test-filename.txt");
assertEquals("Line-1", line);
// Check first line is still available and has not been consumed
assertEquals("Line-1", pushbackReader.readLine());
// Test end of file handling
testText = "";
line = null;
reader = new StringReader(testText);
try
{
line = ComparisonDataFactory.peekFirstLine(new LinePushBackReader(reader), "test-filename.txt");
fail("Expected an IOException for end of file");
}
catch (IOException e)
{
// Expected
assertNotNull(e.getMessage());
assertTrue(e.getMessage().contains("test-filename.txt"));
}
}
/**
* Test the readHeaders method.
* @throws Exception
*/
@Test
public void testReadHeaders() throws Exception
{
// Test reading of comment headers
String testText = "#Comment-1\n# Comment-2\n# Comment 3\nData Line\n";
StringReader reader = new StringReader(testText);
LinePushBackReader pushbackReader = new LinePushBackReader(reader);
List<String> headers = ComparisonDataFactory.readHeaders(pushbackReader, "test-filename.txt");
assertNotNull(headers);
assertEquals(3, headers.size());
assertEquals("#Comment-1", headers.get(0));
assertEquals("# Comment-2", headers.get(1));
assertEquals("# Comment 3", headers.get(2));
assertEquals("Data Line", pushbackReader.readLine());
// Test end of file handling
testText = "";
headers = null;
reader = new StringReader(testText);
try
{
headers = ComparisonDataFactory.readHeaders(pushbackReader, "test-filename.txt");
fail("Expected an IOException for end of file");
}
catch (IOException e)
{
// Expected
assertNotNull(e.getMessage());
assertTrue(e.getMessage().contains("test-filename.txt"));
}
}
/**
* Test loading of Blast web site generated comparison data.
* @throws Exception
*/
@Test
public void testReadComparisonDataForBlastWebSiteHitTable() throws Exception
{
// TBlastx...
// Given
InputStream testFile = ComparisonDataFactoryTest.class.getResourceAsStream(
"/data/act-comparison-files/web-tblastx-comparison-file.txt");
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof BlastWebSiteHitTableComparisonData);
// Check data...
AlignMatch matches [] = result.getMatches();
assertEquals(62, matches.length);
AlignMatch firstDataLine = matches[0];
assertEquals(3678, firstDataLine.getScore());
assertEquals(100, firstDataLine.getPercentID());
assertEquals(2458, firstDataLine.getQuerySequenceStart());
assertEquals(7239, firstDataLine.getQuerySequenceEnd());
assertEquals(3358, firstDataLine.getSubjectSequenceStart());
assertEquals(8139, firstDataLine.getSubjectSequenceEnd());
AlignMatch lastDataLine = matches[61];
assertEquals(20, lastDataLine.getScore());
assertEquals(31, lastDataLine.getPercentID());
assertEquals(1413, lastDataLine.getQuerySequenceStart());
assertEquals(1478, lastDataLine.getQuerySequenceEnd());
assertEquals(6687, lastDataLine.getSubjectSequenceStart());
assertEquals(6752, lastDataLine.getSubjectSequenceEnd());
testFile.close();
// Blastn...
// Given
testFile = ComparisonDataFactoryTest.class.getResourceAsStream(
"/data/act-comparison-files/web-blastn-comparison-file.txt");
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof BlastWebSiteHitTableComparisonData);
// Check data...
matches = result.getMatches();
assertEquals(3, matches.length);
firstDataLine = matches[0];
assertEquals(10072, firstDataLine.getScore());
assertEquals(100, firstDataLine.getPercentID());
assertEquals(2101, firstDataLine.getQuerySequenceStart());
assertEquals(7554, firstDataLine.getQuerySequenceEnd());
assertEquals(3001, firstDataLine.getSubjectSequenceStart());
assertEquals(8454, firstDataLine.getSubjectSequenceEnd());
lastDataLine = matches[2];
assertEquals(1773, lastDataLine.getScore());
assertEquals(95, lastDataLine.getPercentID());
assertEquals(1141, lastDataLine.getQuerySequenceStart());
assertEquals(2100, lastDataLine.getQuerySequenceEnd());
assertEquals(1861, lastDataLine.getSubjectSequenceStart());
assertEquals(2820, lastDataLine.getSubjectSequenceEnd());
testFile.close();
// Empty Blastn file...
// Given
testFile = new ByteArrayInputStream(new byte[0]);
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
try
{
result = ComparisonDataFactory.readComparisonData (comparisonDoc);
fail("Expected IO Excption for an end of file");
}
catch (IOException e)
{
// Expected
assertTrue(e.getMessage().contains("End of file"));
}
testFile.close();
}
/**
* Test loading of SSAHA comparison data.
* @throws Exception
*/
@Test
public void testReadComparisonDataForSSAHA() throws Exception
{
// Check identification of file type...
// Given
StringBuffer dataBuf = new StringBuffer();
dataBuf.append("F\tQueryName1\t10\t20\tSubjectName1\t30\t40\t35\t95\n");
dataBuf.append("F\tQueryName1\t11\t21\tSubjectName1\t31\t41\t36\t96\n");
dataBuf.append("F\tQueryName1\t12\t22\tSubjectName1\t32\t42\t37\t97\n");
StringReader reader = new StringReader(dataBuf.toString());
// When
when( comparisonDoc.getReader() ).thenReturn(reader);
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof SSAHAComparisonData);
// Check data...
AlignMatch matches [] = result.getMatches();
assertEquals(3, matches.length);
AlignMatch firstDataLine = matches[0];
assertEquals(35, firstDataLine.getScore());
assertEquals(95, firstDataLine.getPercentID());
assertEquals(10, firstDataLine.getQuerySequenceStart());
assertEquals(20, firstDataLine.getQuerySequenceEnd());
assertEquals(30, firstDataLine.getSubjectSequenceStart());
assertEquals(40, firstDataLine.getSubjectSequenceEnd());
reader.close();
}
/**
* Test loading of crunch comparison data.
* @throws Exception
*/
@Test
public void testReadComparisonDataForCrunch() throws Exception
{
// Check identification of file type...
// Given
InputStream testFile = ComparisonDataFactoryTest.class.getResourceAsStream(
"/data/act-comparison-files/crunch-comparison-file.crunch");
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof MSPcrunchComparisonData);
// Check data...
AlignMatch matches [] = result.getMatches();
assertEquals(126, matches.length);
AlignMatch firstDataLine = matches[0];
assertEquals(9583, firstDataLine.getScore());
assertEquals(99, firstDataLine.getPercentID());
assertEquals(1474, firstDataLine.getQuerySequenceStart());
assertEquals(6490, firstDataLine.getQuerySequenceEnd());
assertEquals(1474, firstDataLine.getSubjectSequenceStart());
assertEquals(6490, firstDataLine.getSubjectSequenceEnd());
AlignMatch lastDataLine = matches[125];
assertEquals(42, lastDataLine.getScore());
assertEquals(87, lastDataLine.getPercentID());
assertEquals(521, lastDataLine.getQuerySequenceStart());
assertEquals(565, lastDataLine.getQuerySequenceEnd());
assertEquals(66, lastDataLine.getSubjectSequenceStart());
assertEquals(110, lastDataLine.getSubjectSequenceEnd());
testFile.close();
}
/**
* Test loading of Blast m8 formatted comparison data (with no headers).
* @throws Exception
*/
@Test
public void testReadComparisonDataForBlastM8NoHdrs() throws Exception
{
// Given
InputStream testFile = ComparisonDataFactoryTest.class.getResourceAsStream(
"/data/act-comparison-files/blast-m8-comparison-file.txt");
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof BlastM8ComparisonData);
testFile.close();
}
/**
* Test loading of Blast m8 formatted comparison data (with header).
* @throws Exception
*/
@Test
public void testReadComparisonDataForBlastM8WithHdrs() throws Exception
{
// Given
InputStream testFile = ComparisonDataFactoryTest.class.getResourceAsStream(
"/data/act-comparison-files/blast-m8-comparison-file-withhdr.txt");
// When
when( comparisonDoc.getReader() ).thenReturn(new InputStreamReader(testFile));
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
// Then
assertTrue(result instanceof BlastM8ComparisonData);
// Check data...
AlignMatch matches [] = result.getMatches();
assertEquals(3, matches.length);
AlignMatch firstDataLine = matches[0];
assertEquals(5454, firstDataLine.getScore());
assertEquals(100, firstDataLine.getPercentID());
assertEquals(2101, firstDataLine.getQuerySequenceStart());
assertEquals(7554, firstDataLine.getQuerySequenceEnd());
assertEquals(3001, firstDataLine.getSubjectSequenceStart());
assertEquals(8454, firstDataLine.getSubjectSequenceEnd());
AlignMatch lastDataLine = matches[2];
assertEquals(960, lastDataLine.getScore());
assertEquals(100, lastDataLine.getPercentID());
assertEquals(1141, lastDataLine.getQuerySequenceStart());
assertEquals(2100, lastDataLine.getQuerySequenceEnd());
assertEquals(1861, lastDataLine.getSubjectSequenceStart());
assertEquals(2820, lastDataLine.getSubjectSequenceEnd());
testFile.close();
}
/**
* Test response to unrecognised file format.
* @throws Exception
*/
@Test
public void testUnknownFileFormat() throws Exception
{
// Given
String testText = "10\t23\n25\t12\n";
StringReader reader = new StringReader(testText);
// When
when( comparisonDoc.getReader() ).thenReturn(reader);
// Then
try
{
@SuppressWarnings("unused")
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
fail("Expected exception for an unknown file format");
}
catch (Exception e)
{
// Expected
assertEquals("cannot understand the comparison file format", e.getMessage());
}
reader.close();
}
/**
* Test response to an incorrect no. of fields in a Blast web site generated file.
* @throws Exception
*/
@Test
public void testIncorrectFieldNumForBlastWebSiteComparisonData1() throws Exception
{
// Given
StringBuffer dataBuf1 = new StringBuffer();
dataBuf1.append("# blastn\n");
dataBuf1.append("# Iteration: 0\n");
dataBuf1.append("# Query: NC_001954_1_1\n");
dataBuf1.append("# RID: YUYABC86114\n");
dataBuf1.append("# Database: n/a\n");
dataBuf1.append("# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score\n");
dataBuf1.append("# 3 hits found\n");
// Not enough fields
dataBuf1.append("NC_001954_1_1\tNC_001954_1_1\t100.000\t5454\t0\t0\t2101\t7554\t3001\t8454\t0.0\n");
StringReader reader = new StringReader(dataBuf1.toString());
// When
when( comparisonDoc.getReader() ).thenReturn(reader);
// Then
try
{
@SuppressWarnings("unused")
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
fail("Expected exception for incorrect number of fields");
}
catch (Exception e)
{
// Expected
assertTrue(e.getMessage().contains("unexpected number of fields for this line"));
}
reader.close();
}
/**
* Test response to an incorrect no. of fields in a Blast web site generated file.
* @throws Exception
*/
@Test
public void testIncorrectFieldNumForBlastWebSiteComparisonData2() throws Exception
{
// Given
StringBuffer dataBuf1 = new StringBuffer();
dataBuf1.append("# blastn\n");
dataBuf1.append("# Iteration: 0\n");
dataBuf1.append("# Query: NC_001954_1_1\n");
dataBuf1.append("# RID: YUYABC86114\n");
dataBuf1.append("# Database: n/a\n");
dataBuf1.append("# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score\n");
dataBuf1.append("# 3 hits found\n");
// Too many fields
dataBuf1.append("NC_001954_1_1\tNC_001954_1_1\t100.000\t5454\t0\t0\t2101\t7554\t3001\t8454\t0.0\34\23\26\132\n");
StringReader reader = new StringReader(dataBuf1.toString());
// When
when( comparisonDoc.getReader() ).thenReturn(reader);
// Then
try
{
@SuppressWarnings("unused")
ComparisonData result = ComparisonDataFactory.readComparisonData (comparisonDoc);
fail("Expected exception for incorrect number of fields");
}
catch (Exception e)
{
// Expected
assertTrue(e.getMessage().contains("unexpected number of fields for this line"));
}
reader.close();
}
}
src/test/resources/data/act-comparison-files/blast-m8-comparison-file-withhdr.txt 0 → 100644
+ 4
− 0
View file @ aa30c423
# BLASTN 2
NC_001954_1_1 NC_001954_1_1 100.000 5454 0 0 2101 7554 3001 8454 0.0 10072
NC_001954_1_1 NC_001954_1_1 100.000 1141 0 0 1 1141 541 1681 0.0 2108
NC_001954_1_1 NC_001954_1_1 100.000 960 0 0 1141 2100 1861 2820 0.0 1773
src/test/resources/data/act-comparison-files/blast-m8-comparison-file.txt 0 → 100644
+ 3
− 0
View file @ aa30c423
NC_001954_1_1 NC_001954_1_1 100.000 5454 0 0 2101 7554 3001 8454 0.0 10072
NC_001954_1_1 NC_001954_1_1 100.000 1141 0 0 1 1141 541 1681 0.0 2108
NC_001954_1_1 NC_001954_1_1 100.000 960 0 0 1141 2100 1861 2820 0.0 1773
src/test/resources/data/act-comparison-files/crunch-comparison-file.crunch 0 → 100644
+ 126
− 0
View file @ aa30c423
9583 99.00 1474 6490 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1474 6490 SPBC1215 AL096846 S.pombe chromosome II cosmid c1215.
2712 98.00 1 1437 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 1437 SPBC1215 AL096846 S.pombe chromosome II cosmid c1215.
276 99.00 429 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 7588 7734 SPAC1142 AL159951 S.pombe chromosome I cosmid c1142.
274 99.00 429 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 174 319 SPRG5SC K00770 yeast (s.pombe) 5s rrna gene and flanks, clone pspr36.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 48 169 SPRG5S K00569 yeast (s.pombe) 5s rrna gene, clone pym3.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21075 20954 SPCC63 AL049522 S.pombe chromosome III cosmid c63.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 33755 33876 SPCC417 AL035076 S.pombe chromosome III cosmid c417.
228 99.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 22579 22697 SPCC417 AL035076 S.pombe chromosome III cosmid c417.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 31087 30966 SPCC338 AL023781 S.pombe chromosome III cosmid c338.
129 97.00 35 107 big_blast_2_50000_embl_other_c1215.seq.00000001.out 22094 22022 SPCC338 AL023781 S.pombe chromosome III cosmid c338.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 6258 6379 SPBC17A3 AL109652 S.pombe chromosome II cosmid c17A3.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 3214 3335 SPAC5H10 Z49811 S.pombe chromosome I cosmid c5H10.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 8450 8571 SPAC4H3 Z69380 S.pombe chromosome I cosmid c4H3.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 30828 30707 SPAC25B8 AL133225 S.pombe chromosome I cosmid c25B8.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 24568 24447 SPAC1F7 Z67998 S.pombe chromosome I cosmid c1F7.
242 100.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 17220 17099 SPAB4537 AB004537 Schizosaccharomyces pombe 37 kb genomic DNA, clone c213.
240 100.00 453 573 big_blast_2_50000_embl_other_c1215.seq.00000001.out 7867 7747 SPAC926 AL110469 S.pombe chromosome I cosmid c926.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 29615 29496 SPCC965 AL023590 S.pombe chromosome III cosmid c965.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 24228 24347 SPCC24B10 AL157991 S.pombe chromosome III cosmid c24B10.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 5316 5435 SPCC10H11 AL162771 S.pombe chromosome III cosmid c10H11.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 23752 23871 SPBC428 AL034382 S.pombe chromosome II cosmid c428.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 15895 16014 SPBC4 AL121863 S.pombe chromosome II cosmid c4.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 9473 9354 SPBC342 AL096809 S.pombe chromosome II cosmid c342.
238 100.00 456 575 big_blast_2_50000_embl_other_c1215.seq.00000001.out 9665 9546 SPBC21H7 AL023286 S.pombe chromosome II cosmid c21H7.
238 100.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 24026 24145 SPBC1685 AL031154 S.pombe chromosome II cosmid c1685.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 202 320 SPRG5SE K00570 yeast (s.pombe) 5s rrna and asp-trna genes, clone pym116.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 34701 34819 SPBP23A10 AL136535 S.pombe chromosome II p1 p23A10.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 31520 31638 SPBC577 AL110506 S.pombe chromosome II cosmid c577.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 6163 6281 SPBC1677 AL035581 S.pombe chromosome II cosmid c1677.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 18162 18044 SPAC3G9 AL021046 S.pombe chromosome I cosmid c3G9.
236 100.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 119 SPA K01049 Yeast (S.pombe) 5S ribosomal RNA.
234 99.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1664 1543 SPCC188 AL049662 S.pombe chromosome III cosmid c188.
234 99.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 20839 20718 SPCC11E10 AL121783 S.pombe chromosome III cosmid c11E10.
234 99.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 23408 23287 SPBC21D10 AL031536 S.pombe chromosome II cosmid c21D10.
232 99.00 455 575 big_blast_2_50000_embl_other_c1215.seq.00000001.out 3099 3219 SPBC24C6 AL031786 S.pombe chromosome II cosmid c24C6.
230 99.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 200 319 SPRG5SA K00768 yeast (s.pombe) 5s rrna gene and flanks, clone pspr1.
230 99.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 24833 24952 SPBC354 AL022071 S.pombe chromosome II cosmid c354.
230 99.00 455 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 14612 14731 SPAC167 AL035248 S.pombe chromosome I cosmid c167.
228 99.00 456 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 201 319 SPRG5SD K00771 yeast (s.pombe) 5s rrna gene and flanks, clone pspr41.
226 98.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 198 319 SPRG5SB K00769 yeast (s.pombe) 5s rrna gene and flanks, clone pspr11.
226 99.00 455 572 big_blast_2_50000_embl_other_c1215.seq.00000001.out 2544 2661 SPAC24H6 Z54142 S.pombe chromosome I cosmid c24H6.
226 98.00 453 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 13105 12984 SPAC1B1 Z98532 S.pombe chromosome I cosmid c1B1.
222 99.00 457 572 big_blast_2_50000_embl_other_c1215.seq.00000001.out 9084 8969 SPAC1687 AL035064 S.pombe chromosome I cosmid c1687.
220 100.00 454 564 big_blast_2_50000_embl_other_c1215.seq.00000001.out 11460 11350 SPBC14F5 AL023780 S.pombe chromosome II cosmid c14F5.
206 100.00 6387 6490 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 104 SPBC83 AL035536 S.pombe chromosome II cosmid c83.
163 100.00 1 82 big_blast_2_50000_embl_other_c1215.seq.00000001.out 82 1 SPAB4534 AB004534 Schizosaccharomyces pombe 38 kb genomic DNA, clone 1750.
157 100.00 496 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 79 SPBC725 AL034352 S.pombe chromosome II cosmid c725.
157 100.00 496 574 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 79 SPBC530 AL023634 S.pombe chromosome II cosmid c530.
103 100.00 455 506 big_blast_2_50000_embl_other_c1215.seq.00000001.out 52 1 SPRHP9 Y09431 S.pombe rhp9 gene
93 85.00 463 575 big_blast_2_50000_embl_other_c1215.seq.00000001.out 14821 14716 SPBC609 AL035226 S.pombe chromosome II cosmid c609.
65 89.00 456 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 57 UURNA1 X00998 Urechis unicinctus 5S rRNA sequence
58 95.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 PGRNA01 X00994 Phascolopsis gouldii 5S rRNA sequence
58 95.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 904 868 CFRRN285 X06056 Calanus finmarchicus DNA for 23S and 5S rRNA
56 93.00 477 516 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1113 1074 SPBC1778 AL049489 S.pombe chromosome II cosmid c1778.
52 100.00 6059 6084 big_blast_2_50000_embl_other_c1215.seq.00000001.out 233479 233504 AE003531 AE003531 Drosophila melanogaster genomic scaffold 142000013386050 section 37 of 54, complete sequence.
50 92.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 PRRRN5S X01550 Planocera reticulata 5S ribosomal RNA
50 92.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 EGRN01 X00022 Ribbon worm Emplectonema gracile 5S rRNA (Short)
50 94.00 480 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 25 57 AMRRN5S X01518 Acyrthosiphon magnoliae (aphid) 5S ribosomal RNA
50 89.00 461 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 6 58 CR1619 D10528 Candida rugosa 5S rRNA.
50 88.00 521 569 big_blast_2_50000_embl_other_c1215.seq.00000001.out 66 114 AERRA K03161 Agaricus edulis 5S ribosomal RNA (5S rRNA).
48 96.00 2466 2493 big_blast_2_50000_embl_other_c1215.seq.00000001.out 10841 10814 AC010292 AC010292 Homo sapiens chromosome 5 clone CTB-131H22, complete sequence.
46 85.00 458 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 5564 5510 PDHISTCL X53330 P.dumerilii histone gene cluster for core histones H2A, H2B, H3 and H4
46 100.00 4802 4824 big_blast_2_50000_embl_other_c1215.seq.00000001.out 28075 28053 HSU165H7 Z70225 Human DNA sequence from cosmid U165H7, between markers DXS366 and DXS87 on chromosome X.
46 88.00 526 568 big_blast_2_50000_embl_other_c1215.seq.00000001.out 72 114 TDRRA M58385 Taphrina deformans 5S ribosomal RNA.
46 96.00 487 513 big_blast_2_50000_embl_other_c1215.seq.00000001.out 3 29 SPRRAAS M19951 Schizosaccharomyces pombe 5S ribosomal RNA gene, partial sequence.
44 100.00 4816 4837 big_blast_2_50000_embl_other_c1215.seq.00000001.out 88073 88052 AC084760 AC084760 Gallus gallus clone 65N20, complete sequence.
44 88.00 57 98 big_blast_2_50000_embl_other_c1215.seq.00000001.out 69197 69238 CHPTTRPG D17510 Pinus thunbergii chloroplast DNA, complete sequence.
44 88.00 57 98 big_blast_2_50000_embl_other_c1215.seq.00000001.out 48563 48522 CHNTXX Z00044 Nicotiana tabacum chloroplast genome DNA
44 88.00 57 98 big_blast_2_50000_embl_other_c1215.seq.00000001.out 138 97 CHNTTB2 M16897 Tobacco Thr-tRNA gene.
44 88.00 57 98 big_blast_2_50000_embl_other_c1215.seq.00000001.out 14879 14920 AP002983 AP002983 Lotus japonicus chloroplast DNA, complete genome.
44 88.00 57 98 big_blast_2_50000_embl_other_c1215.seq.00000001.out 46263 46222 AP000423 AP000423 Arabidopsis thaliana chloroplast genomic DNA, complete sequence, strain:Columbia.
44 100.00 893 914 big_blast_2_50000_embl_other_c1215.seq.00000001.out 49861 49882 HSEVMHC X87344 H.sapiens DMA, DMB, HLA-Z1, IPP2, LMP2, TAP1, LMP7, TAP2, DOB, DQB2 and RING8, 9, 13 and 14 genes
44 100.00 6061 6082 big_blast_2_50000_embl_other_c1215.seq.00000001.out 143317 143296 HS377H14 AL022723 Human DNA sequence from clone 377H14 on chromosome 6p21.32-22.1. Contains the HLA-G gene for major histocompatibility complex, class I, G (HLA 6.0) two MHC class I pseudogenes, an RPL7A (60S Ribosomal Protein L7A) pseudogene, a gene for a novel MHC class 1 protein, an interferon-inducible protein 1-8U pseudogene, an RPL23A (60S Ribosomal Protein L23A) pseudogene, an HCGIX pseudogene, an MICB or PERB11.1 pseudogene,the HLA-F gene for major histocompatibility complex, class I, F (CDA12), and four P5-1 pseudogenes. Contains EST, STSs, GSS and six putative CpG islands.
44 100.00 1237 1258 big_blast_2_50000_embl_other_c1215.seq.00000001.out 3149 3128 AP001207 AP001207 Homo sapiens genomic DNA, chromosome 8q23, clone:KB1562D12.
44 100.00 1237 1258 big_blast_2_50000_embl_other_c1215.seq.00000001.out 201930 201909 AP000426 AP000426 Homo sapiens genomic DNA, chromosome 8q23, clone:KB1107E3.
44 93.00 2454 2483 big_blast_2_50000_embl_other_c1215.seq.00000001.out 75294 75323 AC023426 AC023426 Homo sapiens 12 BAC RP11-396L8 (Roswell Park Cancer Institute Human BAC Library) complete sequence.
44 100.00 6061 6082 big_blast_2_50000_embl_other_c1215.seq.00000001.out 34756 34735 AC004213 AC004213 Homo sapiens clone UWGC:y19c060 from 6p21, complete sequence.
44 86.00 521 570 big_blast_2_50000_embl_other_c1215.seq.00000001.out 364 413 AI5SRRNA2 X99089 A.immersus 5S rRNA gene, b2-type
42 100.00 1245 1265 big_blast_2_50000_embl_other_c1215.seq.00000001.out 12979 12959 BBU43414 U43414 Borrelia burgdorferi linear plasmid lp16 DNA, complete sequence.
42 100.00 2454 2474 big_blast_2_50000_embl_other_c1215.seq.00000001.out 278691 278671 AP001119 AP001119 Buchnera sp. APS genomic DNA, complete sequence, segment 2/2.
42 100.00 1245 1265 big_blast_2_50000_embl_other_c1215.seq.00000001.out 12951 12931 AE000793 AE000793 Borrelia burgdorferi plasmid lp17, complete plasmid sequence.
42 100.00 818 838 big_blast_2_50000_embl_other_c1215.seq.00000001.out 2471 2451 OSU77637 U77637 Oryza sativa class III ADH enzyme (AdhIII) gene, complete cds.
42 96.00 1241 1265 big_blast_2_50000_embl_other_c1215.seq.00000001.out 79773 79797 H0505A02 AL512543 Oryza sativa genomic DNA, chromosome 4, BAC clone: H0505A02, complete sequence
42 93.00 343 371 big_blast_2_50000_embl_other_c1215.seq.00000001.out 29118 29146 AB018121 AB018121 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone: MXE2.
42 84.00 456 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 57 SSRRAB K02349 Jellyfish (Spirocodon saltatrix) 5S ribosomal RNA.
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 PCRN5SA X13039 Philosamia cynthia ricini 5S rRNA
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 PCRN5S K02354 Philosamia cythia ricini (silkworm) 5S ribosomal RNA.
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 OV5SRRN X06835 Octopus vulgaris 5S rRNA
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 ME5SRNA J01869 Mussel (Mytilus edulis) 5S ribosomal RNA.
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 LGRNO1 X00020 Ribbon worm Lineus geniculatus 5S rRNA
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 HSRRN5S X01535 Hymeniacidon sanguinea 5S ribosomal RNA
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 HJRN01 V00475 Halichondria japonica 5S ribosomal RNA (complete sequence).
42 84.00 456 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 57 EARRN5S X03911 Enchytraeus albidus 5S rRNA
42 100.00 6340 6360 big_blast_2_50000_embl_other_c1215.seq.00000001.out 25954 25974 CEK02B12 Z75711 Caenorhabditis elegans cosmid K02B12
42 100.00 1213 1233 big_blast_2_50000_embl_other_c1215.seq.00000001.out 5436 5456 CEF14B8 U28737 Caenorhabditis elegans cosmid F14B8.
42 84.00 456 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 57 CED132199 AJ132199 Cerastoderma edule 5S rRNA gene and nontranscribed spacer, clone 4
42 84.00 456 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 1 57 CED132198 AJ132198 Cerastoderma edule 5S rRNA gene and nontranscribed spacer, clone 3
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 BN5SRRN X06834 Bugula neritina (moss-animal) 5S rRNA
42 100.00 5756 5776 big_blast_2_50000_embl_other_c1215.seq.00000001.out 2219 2239 BMU86876 U86876 Bombyx mori chitinase-like protein mRNA, complete cds.
42 89.00 476 512 big_blast_2_50000_embl_other_c1215.seq.00000001.out 21 57 APRN5SA X13035 Antheraea pernyi 5S rRNA
42 100.00 5756 5776 big_blast_2_50000_embl_other_c1215.seq.00000001.out 2256 2276 AF326596 AF326596 Bombyx mandarina chitinase mRNA, complete cds.
42 100.00 136 156 big_blast_2_50000_embl_other_c1215.seq.00000001.out 6370 6350 AC084626 AC084626 Caenorhabditis briggsae cosmid G45C20, complete sequence.
42 100.00 6091 6111 big_blast_2_50000_embl_other_c1215.seq.00000001.out 27211 27231 AC006830 AC006830 Caenorhabditis elegans cosmid ZK105, complete sequence.
42 100.00 5756 5776 big_blast_2_50000_embl_other_c1215.seq.00000001.out 2225 2245 AB052914 AB052914 Bombyx mori chiB mRNA for chitinase precursor, complete cds.
42 100.00 1395 1415 big_blast_2_50000_embl_other_c1215.seq.00000001.out 145576 145596 HSMX1A AL442166 Homo sapiens chromosome 21 from 5 PACs and 5 Cosmids map 21q22.2,D21S349-MX1; segment 1/2
42 100.00 6065 6085 big_blast_2_50000_embl_other_c1215.seq.00000001.out 70745 70765 HS994L9 AL034554 Human DNA sequence from clone 994L9 on chromosome 20p12.3-13 Contains STS and GSSs.
42 100.00 1395 1415 big_blast_2_50000_embl_other_c1215.seq.00000001.out 173941 173961 HS21C084 AL163284 Homo sapiens chromosome 21 segment HS21C084.
42 100.00 5172 5192 big_blast_2_50000_embl_other_c1215.seq.00000001.out 8899 8879 HS21C013 AL163213 Homo sapiens chromosome 21 segment HS21C013.
42 96.00 3691 3715 big_blast_2_50000_embl_other_c1215.seq.00000001.out 222756 222780 AP001732 AP001732 Homo sapiens genomic DNA, chromosome 21q, section 76/105.
42 96.00 334 358 big_blast_2_50000_embl_other_c1215.seq.00000001.out 234259 234235 AP001677 AP001677 Homo sapiens genomic DNA, chromosome 21q, section 21/105.
42 96.00 3691 3715 big_blast_2_50000_embl_other_c1215.seq.00000001.out 97170 97194 AP001038 AP001038 Homo sapiens genomic DNA, chromosome 21, clone:P178O22, ERG-ETS2 region.
42 96.00 334 358 big_blast_2_50000_embl_other_c1215.seq.00000001.out 117565 117541 AP000946 AP000946 Homo sapiens genomic DNA, chromosome 21q21.1-q21.2, clone:B335N5, LL56-APP region.
42 100.00 6106 6126 big_blast_2_50000_embl_other_c1215.seq.00000001.out 179419 179439 AP000810 AP000810 Homo sapiens genomic DNA, chromosome 11q, clone:RP11-765H23.
42 100.00 5172 5192 big_blast_2_50000_embl_other_c1215.seq.00000001.out 94404 94384 AP000473 AP000473 Homo sapiens genomic DNA, chromosome 21q21.1-q21.2, clone:B291N6, LL56-APP region.
42 96.00 1801 1825 big_blast_2_50000_embl_other_c1215.seq.00000001.out 6090 6114 AL355365 AL355365 Human DNA sequence from clone RP11-361F15 on chromosome 6
42 96.00 5531 5555 big_blast_2_50000_embl_other_c1215.seq.00000001.out 79645 79669 AL354861 AL354861 Human DNA sequence from clone RP11-180I4 on chromosome 9
42 100.00 1 21 big_blast_2_50000_embl_other_c1215.seq.00000001.out 28666 28686 AL139378 AL139378 Human DNA sequence from clone RP11-271B5 on chromosome 13 Contains a gene for a protein similar to ribosomal protein S7, the FGF9 (fibroblast growth factor 9 (glia-activating factor)) gene, ESTs, STSs, GSSs and CpG islands.
42 100.00 5783 5803 big_blast_2_50000_embl_other_c1215.seq.00000001.out 15259 15279 AL139163 AL139163 Human DNA sequence from clone RP11-523O15 on chromosome 20 Contains GSSs and STSs.
42 100.00 3803 3823 big_blast_2_50000_embl_other_c1215.seq.00000001.out 20782 20802 AL136301 AL136301 Human DNA sequence from clone RP11-195L15 on chromosome 13
42 91.00 5752 5784 big_blast_2_50000_embl_other_c1215.seq.00000001.out 74511 74543 AL133462 AL133462 Human DNA sequence from clone RP11-108A16 on chromosome 20 Contains ESTs, STSs and GSSs.
42 96.00 334 358 big_blast_2_50000_embl_other_c1215.seq.00000001.out 119422 119446 AF238375 AF238375 Homo sapiens chromosome 21 clone BAC 49B5 map 21q21, complete sequence.
42 100.00 1242 1262 big_blast_2_50000_embl_other_c1215.seq.00000001.out 42069 42089 AF130342 AF130342 Homo sapiens chromosome 8 clone PAC 87.1 map 8q24.1, complete sequence.
42 91.00 5752 5784 big_blast_2_50000_embl_other_c1215.seq.00000001.out 49339 49371 AC012380 AC012380 Genomic Sequence For Homo sapiens Clone 125H5, Chromosome 20, complete sequence.
42 93.00 1230 1258 big_blast_2_50000_embl_other_c1215.seq.00000001.out 135503 135475 AC007392 AC007392 Homo sapiens BAC clone RP11-444B4 from 2, complete sequence.
42 100.00 1414 1434 big_blast_2_50000_embl_other_c1215.seq.00000001.out 4290 4310 PCAROMX L18918 Pneumocystis carinii pentafunctional enzyme (arom) gene, complete cds.
42 87.00 521 565 big_blast_2_50000_embl_other_c1215.seq.00000001.out 66 110 CH1457 D10531 Cryptococcus humicolus 5S rRNA.
src/test/resources/data/act-comparison-files/web-blastn-comparison-file-empty.txt 0 → 100644
+ 9
− 0
View file @ aa30c423
# blastn
# Iteration: 0
# Query: NC_001954_1_1
# RID: YUYABC86114
# Database: n/a
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 0 hits found
src/test/resources/data/act-comparison-files/web-blastn-comparison-file.txt 0 → 100644
+ 12
− 0
View file @ aa30c423
# blastn
# Iteration: 0
# Query: NC_001954_1_1
# RID: YUYABC86114
# Database: n/a
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 3 hits found
NC_001954_1_1 NC_001954_1_1 100.000 5454 0 0 2101 7554 3001 8454 0.0 10072
NC_001954_1_1 NC_001954_1_1 100.000 1141 0 0 1 1141 541 1681 0.0 2108
NC_001954_1_1 NC_001954_1_1 95.000 960 0 0 1141 2100 1861 2820 0.0 1773
src/test/resources/data/act-comparison-files/web-tblastx-comparison-file.txt 0 → 100644
+ 71
− 0
View file @ aa30c423
# tblastx
# Iteration: 0
# Query: NC_001954_1_1
# RID: YUVM0CMY114
# Database: n/a
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, % positives, query/sbjct frames
# 1 hits found
NC_001954_1_1 NC_001954_1_1 100.000 1594 0 0 2458 7239 3358 8139 0.0 3678 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 1361 0 0 3471 7553 4371 8453 0.0 3248 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 936 0 0 7552 4745 8452 5645 0.0 2132 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 99.429 875 5 0 4708 2084 5608 2984 0.0 1989 99.66 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 782 0 0 7554 5209 8454 6109 0.0 1827 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 744 0 0 2102 4333 3002 5233 0.0 1743 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 715 0 0 4247 2103 5147 3003 0.0 1639 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 633 0 0 7553 5655 8453 6555 0.0 1510 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 569 0 0 5169 3463 6069 4363 0.0 1279 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 432 0 0 5609 4314 6509 5214 0.0 1032 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 420 0 0 6293 7552 7193 8452 0.0 993 100.00 2/2
NC_001954_1_1 NC_001954_1_1 99.742 387 1 0 2100 3260 3000 4160 0.0 929 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 339 0 0 49 1065 589 1605 0.0 732 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 326 0 0 4388 5365 5288 6265 0.0 663 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 278 0 0 5411 6244 6311 7144 0.0 630 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 236 0 0 3171 2464 4071 3364 0.0 521 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 216 0 0 1139 492 1679 1032 0.0 511 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 219 0 0 1157 1813 1877 2533 0.0 459 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 186 0 0 1698 1141 2418 1861 0.0 456 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 187 0 0 1702 1142 2422 1862 0.0 432 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 189 0 0 1087 521 1627 1061 0.0 430 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 175 0 0 539 1063 1079 1603 0.0 422 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 166 0 0 1603 2100 2323 2820 0.0 403 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 172 0 0 1053 538 1593 1078 0.0 358 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 134 0 0 1302 1703 2022 2423 0.0 341 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 152 0 0 457 2 997 542 0.0 341 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 129 0 0 387 1 927 541 0.0 315 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 137 0 0 2099 1689 2819 2409 0.0 301 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 119 0 0 2103 1747 2823 2467 0.0 296 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 121 0 0 1737 2099 2457 2819 0.0 282 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 121 0 0 437 75 977 615 0.0 282 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 117 0 0 1646 1296 2366 2016 0.0 268 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 94.737 114 6 0 2421 2080 3321 2980 0.0 262 96.49 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 107 0 0 146 466 686 1006 0.0 239 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 106 0 0 2101 2418 3001 3318 0.0 214 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 87 0 0 7294 7554 8194 8454 0.0 209 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 81 0 0 3 245 543 785 0.0 204 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 83 0 0 1297 1545 2017 2265 0.0 198 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 86 0 0 1990 1733 2710 2453 0.0 193 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 85 0 0 1847 2101 2567 2821 0.0 170 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 88 0 0 300 563 840 1103 0.0 169 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 69 0 0 3426 3220 4326 4120 0.0 163 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 100.000 45 0 0 3297 3431 4197 4331 0.0 121 100.00 3/3
NC_001954_1_1 NC_001954_1_1 97.436 39 1 0 1138 1254 1858 1974 0.0 94.1 100.00 1/1
NC_001954_1_1 NC_001954_1_1 100.000 34 0 0 1241 1140 1961 1860 0.0 82.6 100.00 -2/-2
NC_001954_1_1 NC_001954_1_1 100.000 31 0 0 768 860 1308 1400 0.0 78.5 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 30 0 0 906 995 1446 1535 0.0 69.3 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 23 0 0 2098 2030 2818 2750 0.0 59.3 100.00 -3/-3
NC_001954_1_1 NC_001954_1_1 100.000 23 0 0 627 695 1167 1235 0.0 55.6 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 31 0 0 2 94 542 634 0.0 51.5 100.00 2/2
NC_001954_1_1 NC_001954_1_1 100.000 17 0 0 1203 1253 1923 1973 0.0 47.8 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 34 0 0 1041 1142 1581 1682 0.0 45.1 100.00 3/3
NC_001954_1_1 NC_001954_1_1 100.000 15 0 0 465 421 1005 961 0.0 38.6 100.00 -1/-1
NC_001954_1_1 NC_001954_1_1 66.667 9 3 0 6028 6054 6871 6897 0.0 20.3 77.78 1/1
NC_001954_1_1 NC_001954_1_1 66.667 9 3 0 5971 5997 6928 6954 0.0 20.3 77.78 1/1
NC_001954_1_1 NC_001954_1_1 21.053 19 15 0 7349 7293 6604 6548 0.0 19.9 52.63 -2/-3
NC_001954_1_1 NC_001954_1_1 27.273 33 24 0 2856 2758 4756 4658 0.0 19.9 54.55 -1/-3
NC_001954_1_1 NC_001954_1_1 27.273 33 24 0 3856 3758 3756 3658 0.0 19.9 54.55 -3/-1
NC_001954_1_1 NC_001954_1_1 36.000 25 16 0 611 685 4365 4439 0.035 28.6 56.00 2/3
NC_001954_1_1 NC_001954_1_1 38.095 21 13 0 3477 3539 1163 1225 0.17 26.3 61.90 3/2
NC_001954_1_1 NC_001954_1_1 31.818 22 15 0 5787 5852 2133 2198 7.8 20.8 54.55 3/3
NC_001954_1_1 NC_001954_1_1 31.818 22 15 0 1413 1478 6687 6752 7.8 20.8 54.55 3/3
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