Examples with Orientation org.dishevelled.bio.assembly.gfa2.Orientation used on opensource projects

Example 1 with Orientation

use of org.dishevelled.bio.assembly.gfa2.Orientation in project dishevelled by heuermh.

the class ImportGfa1Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 1.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final ListMultimap<String, Traversal> traversalsByPathName = ArrayListMultimap.create();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa1Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final List<Path> paths = new ArrayList<Path>();
    final List<Link> links = new ArrayList<Link>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream paths and links, looking for reverse orientation references
        stream(readable, new Gfa1Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            protected boolean path(final Path path) {
                for (Reference reference : path.getSegments()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }

            @Override
            protected boolean link(final Link link) {
                putIfAbsent(link.getSource());
                putIfAbsent(link.getTarget());
                links.add(link);
                return true;
            }

            @Override
            protected boolean traversal(final Traversal traversal) {
                traversalsByPathName.put(traversal.getPathName(), traversal);
                return true;
            }
        });
    }
    logger.info("read {} segments, {} links, {} paths, and {} traversals from {}", new Object[] { segmentsById.size(), links.size(), paths.size(), traversalsByPathName.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLengthOpt().orElse(null);
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from links ...");
    for (Link link : links) {
        String sourceId = link.getSource().getId();
        String sourceOrientation = link.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = link.getTarget().getId();
        String targetOrientation = link.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, link.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "overlap", String.class, link.getOverlapOpt().orElse(null));
        setValue(edgeTable, edgeRow, "readCount", Integer.class, link.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, link.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, link.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, link.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, link.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted links to " + links.size() + " edges");
    nodes.clear();
    links.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
        assemblyModel.setPaths(paths, traversalsByPathName);
    }
}

Example 2 with Orientation

use of org.dishevelled.bio.assembly.gfa2.Orientation in project dishevelled by heuermh.

the class ImportGfa2Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 2.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa2Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final List<Edge> edges = new ArrayList<Edge>();
    final List<Gap> gaps = new ArrayList<Gap>();
    final List<Path> paths = new ArrayList<Path>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream edges, gaps, and paths, looking for reverse orientation references
        stream(readable, new Gfa2Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            public boolean edge(final Edge edge) {
                putIfAbsent(edge.getSource());
                putIfAbsent(edge.getTarget());
                edges.add(edge);
                return true;
            }

            @Override
            public boolean gap(final Gap gap) {
                putIfAbsent(gap.getSource());
                putIfAbsent(gap.getTarget());
                gaps.add(gap);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                for (Reference reference : path.getReferences()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }
        });
    }
    logger.info("read {} segments, {} edges, {} gaps, and {} paths from {}", new Object[] { segmentsById.size(), edges.size(), gaps.size(), paths.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLength();
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from edges and gaps ...");
    for (Edge edge : edges) {
        String sourceId = edge.getSource().getId();
        String sourceOrientation = edge.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = edge.getTarget().getId();
        String targetOrientation = edge.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge cyEdge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(cyEdge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, edge.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "sourceStart", String.class, edge.getSourceStart().toString());
        setValue(edgeTable, edgeRow, "sourceEnd", String.class, edge.getSourceEnd().toString());
        setValue(edgeTable, edgeRow, "targetStart", String.class, edge.getTargetStart().toString());
        setValue(edgeTable, edgeRow, "targetEnd", String.class, edge.getTargetEnd().toString());
        setValue(edgeTable, edgeRow, "alignment", String.class, edge.hasAlignment() ? edge.getAlignment().toString() : null);
        setValue(edgeTable, edgeRow, "readCount", Integer.class, edge.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, edge.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, edge.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, edge.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, edge.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted edges to " + edges.size() + " edges");
    for (Gap gap : gaps) {
        String sourceId = gap.getSource().getId();
        String sourceOrientation = gap.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = gap.getTarget().getId();
        String targetOrientation = gap.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, gap.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "gap");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "distance", Integer.class, gap.getDistance());
        setValue(edgeTable, edgeRow, "variance", Integer.class, gap.getVarianceOpt().orElse(null));
    }
    logger.info("converted gaps to " + gaps.size() + " edges");
    nodes.clear();
    edges.clear();
    gaps.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
    // todo: convert to gfa1 paths?
    // note paths in gfa2 can have references to segments, edges, or other groups
    // assemblyModel.setPaths(paths, traversalsByPathName);
    }
}