From f6420b586738e7edcda6b4c310d0ba2c8f8cee52 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 5 Apr 2011 16:04:43 +0000
Subject: [PATCH] add option to count reads for selected features
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15867 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/alignment/BamUtils.java | 217 ++++++++++++++++++
.../artemis/components/alignment/BamView.java | 29 ++-
2 files changed, 245 insertions(+), 1 deletion(-)
create mode 100644 uk/ac/sanger/artemis/components/alignment/BamUtils.java
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
new file mode 100644
index 000000000..b786157bc
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -0,0 +1,217 @@
+/* BamUtils
+ *
+ * created: 2011
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2011 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.components.alignment;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CloseableIterator;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.components.FileViewer;
+
+class BamUtils
+{
+ /**
+ *
+ * @param features
+ * @param refName
+ * @param samFileReaderHash
+ * @param bamList
+ * @param seqNames
+ * @param offsetLengths
+ * @param concatSequences
+ * @param seqLengths
+ * @param samRecordFlagPredicate
+ * @param samRecordMapQPredicate
+ * @param contained
+ * @param useIntrons
+ */
+ protected static void countReads(final FeatureVector features,
+ final String refName,
+ final Hashtable<String, SAMFileReader> samFileReaderHash,
+ final List<String> bamList,
+ final Vector<String> seqNames,
+ final Hashtable<String, Integer> offsetLengths,
+ final boolean concatSequences,
+ final Hashtable<String, Integer> seqLengths,
+ final SAMRecordFlagPredicate samRecordFlagPredicate,
+ final SAMRecordMapQPredicate samRecordMapQPredicate,
+ final boolean contained,
+ final boolean useIntrons)
+ {
+ Hashtable<String, List<Integer>> featureReadCount = new Hashtable<String, List<Integer>>();
+ for(int i=0; i<features.size(); i++)
+ {
+ Feature f = features.elementAt(i);
+
+ int start = f.getFirstBase();
+ int end = f.getLastBase();
+ List<Integer> sampleCounts = new Vector<Integer>();
+
+ for(String bam : bamList)
+ {
+ int cnt = 0;
+ if(!useIntrons && f.getSegments().size() > 1)
+ {
+ for(int j=0; j<f.getSegments().size(); j++)
+ {
+ start = f.getSegments().elementAt(j).getStart().getPosition();
+ end = f.getSegments().elementAt(j).getEnd().getPosition();
+ cnt += getCount(start, end, bam, refName, samFileReaderHash,
+ seqNames, offsetLengths, concatSequences, seqLengths,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+ }
+ }
+ else
+ cnt = getCount(start, end, bam, refName, samFileReaderHash,
+ seqNames, offsetLengths, concatSequences, seqLengths,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+
+ sampleCounts.add(cnt);
+ }
+
+ featureReadCount.put(f.getSystematicName(), sampleCounts);
+ }
+
+ StringBuffer buff = new StringBuffer();
+ buff.append("\t");
+ for(String bam : bamList)
+ buff.append(bam+"\t");
+ buff.append("\n");
+
+ for (String fId : featureReadCount.keySet() ) {
+ buff.append(fId+"\t");
+ List<Integer> cnts = featureReadCount.get(fId);
+ for(int i=0; i<cnts.size(); i++)
+ buff.append(cnts.get(i)+(i<cnts.size()-1 ? "\t" : ""));
+ buff.append("\n");
+ }
+
+ FileViewer viewer = new FileViewer ("Read Count", true);
+ viewer.getTextPane().setText(buff.toString());
+ }
+
+ /**
+ * Count the reads in a range.
+ * @param start
+ * @param end
+ * @param bam
+ * @param refName
+ * @param samFileReaderHash
+ * @param seqNames
+ * @param offsetLengths
+ * @param concatSequences
+ * @param seqLengths
+ * @param samRecordFlagPredicate
+ * @param samRecordMapQPredicate
+ * @param contained
+ * @return
+ */
+ private static int getCount(
+ final int start,
+ final int end,
+ final String bam,
+ final String refName,
+ final Hashtable<String, SAMFileReader> samFileReaderHash,
+ final Vector<String> seqNames,
+ final Hashtable<String, Integer> offsetLengths,
+ final boolean concatSequences,
+ final Hashtable<String, Integer> seqLengths,
+ final SAMRecordFlagPredicate samRecordFlagPredicate,
+ final SAMRecordMapQPredicate samRecordMapQPredicate,
+ final boolean contained)
+ {
+ int cnt = 0;
+ if(concatSequences)
+ {
+ int len = 0;
+ int lastLen = 1;
+ for(String name : seqNames)
+ {
+ int thisLength = seqLengths.get(name);
+ len += thisLength;
+
+ if( (lastLen >= start && lastLen < end) ||
+ (len >= start && len < end) ||
+ (start >= lastLen && start < len) ||
+ (end >= lastLen && end < len) )
+ {
+ int offset = offsetLengths.get(name);
+ int thisStart = start - offset;
+ if(thisStart < 1)
+ thisStart = 1;
+ int thisEnd = end - offset;
+ if(thisEnd > thisLength)
+ thisEnd = thisLength;
+
+ cnt = count(bam, samFileReaderHash, name, thisStart, thisEnd,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+
+ }
+ lastLen = len;
+ }
+ }
+ else
+ {
+ cnt = count(bam, samFileReaderHash, refName, start, end,
+ samRecordFlagPredicate, samRecordMapQPredicate, contained);
+ }
+ return cnt;
+ }
+
+ private static int count(String bam,
+ Hashtable<String, SAMFileReader> samFileReaderHash,
+ String refName,
+ int start,
+ int end,
+ SAMRecordFlagPredicate samRecordFlagPredicate,
+ SAMRecordMapQPredicate samRecordMapQPredicate,
+ boolean contained)
+ {
+ int cnt = 0;
+ SAMFileReader inputSam = samFileReaderHash.get(bam);
+ final CloseableIterator<SAMRecord> it = inputSam.query(refName, start, end, contained);
+
+ while ( it.hasNext() )
+ {
+ SAMRecord samRecord = it.next();
+ if( samRecordFlagPredicate == null ||
+ !samRecordFlagPredicate.testPredicate(samRecord))
+ {
+ if(samRecordMapQPredicate == null ||
+ samRecordMapQPredicate.testPredicate(samRecord))
+ {
+ cnt++;
+ }
+ }
+ }
+ it.close();
+ return cnt;
+ }
+}
+
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 46557a457..c60eef4f8 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -67,6 +67,7 @@ import java.util.List;
import java.util.Vector;
import javax.swing.BorderFactory;
+import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
@@ -1977,7 +1978,7 @@ public class BamView extends JPanel
private void createMenus(JComponent menu)
{
- final JMenuItem addBam = new JMenuItem("Add Bam ...");
+ final JMenuItem addBam = new JMenuItem("Add BAM ...");
menu.add(addBam);
addBam.addActionListener(new ActionListener()
{
@@ -2000,6 +2001,32 @@ public class BamView extends JPanel
bamFilesMenu.setFont(addBam.getFont());
menu.add(bamFilesMenu);
+
+ final JMenu analyse = new JMenu("Analyse");
+ menu.add(analyse);
+ final JMenuItem readCount = new JMenuItem("Read count for selected features ...");
+ analyse.add(readCount);
+ readCount.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ FeatureVector features = feature_display.getSelection().getAllFeatures();
+
+ JCheckBox overlap = new JCheckBox("Include all overlapping reads", true);
+ overlap.setToolTipText("Include reads that partially overlap the feature");
+ JCheckBox spliced = new JCheckBox("Introns included", true);
+ Box yBox = Box.createVerticalBox();
+ yBox.add(overlap);
+ yBox.add(spliced);
+ JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
+
+ BamUtils.countReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
+ seqNames, offsetLengths, concatSequences, seqLengths,
+ samRecordFlagPredicate, samRecordMapQPredicate,
+ !overlap.isSelected(), spliced.isSelected());
+ }
+ });
+
for(int i=0; i<bamList.size(); i++)
addToViewMenu(i);
--
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