Examples with InvalidGenomicCoordsException exceptions.InvalidGenomicCoordsException used on opensource projects

Example 1 with InvalidGenomicCoordsException

use of exceptions.InvalidGenomicCoordsException in project ASCIIGenome by dariober.

the class GenomicCoords method parseStringToGenomicCoords.

/**
 * Parse string to return coordinates. This method simply populates the fields chrom, from, to by
 * parsing the input string.
 * This object can't be used as such as there is no check for valid input. It should be used only by the constructor.
 * @return
 * @throws InvalidGenomicCoordsException
 * @throws IOException
 */
private GenomicCoords parseStringToGenomicCoords(String x) throws InvalidGenomicCoordsException, IOException {
    // Default start/end coords.
    Integer from = 1;
    Integer to = this.getTerminalWidth();
    GenomicCoords xgc = new GenomicCoords(this.getTerminalWidth());
    if (x == null || x.isEmpty()) {
        x = "Undefined_contig";
    }
    x = x.trim();
    int nsep = StringUtils.countMatches(x, ":");
    if (nsep == 0) {
        // Only chrom present. It will not handle well chrom names containing ':'
        xgc.chrom = x.trim();
        xgc.from = from;
        xgc.to = to;
        if (xgc.samSeqDict != null && xgc.to > samSeqDict.getSequence(xgc.chrom).getSequenceLength()) {
            xgc.to = samSeqDict.getSequence(xgc.chrom).getSequenceLength();
        }
    } else {
        xgc.chrom = StringUtils.substringBeforeLast(x, ":").trim();
        // Strip chromosome name, remove commas from integers.
        String fromTo = StringUtils.substringAfterLast(x, ":").replaceAll(",", "").trim();
        nsep = StringUtils.countMatches(fromTo, "-");
        if (nsep == 0) {
            // Only start position given
            xgc.from = Integer.parseInt(StringUtils.substringBefore(fromTo, "-").trim());
            xgc.to = xgc.from + this.getTerminalWidth() - 1;
        } else if (nsep == 1) {
            // From and To positions given.
            xgc.from = Integer.parseInt(StringUtils.substringBefore(fromTo, "-").trim());
            xgc.to = Integer.parseInt(StringUtils.substringAfter(fromTo, "-").trim());
        } else {
            InvalidGenomicCoordsException e = new InvalidGenomicCoordsException();
            System.err.println("\nUnexpected format for region " + x + "\n");
            e.printStackTrace();
            throw e;
        }
    }
    return xgc;
}

Example 2 with InvalidGenomicCoordsException

use of exceptions.InvalidGenomicCoordsException in project ASCIIGenome by dariober.

the class GenomicCoords method getChromIdeogram.

/**
 * Produce a string representation of the current position on the chromosome
 * @param nDist: Distance between labels
 * @throws IOException
 * @throws InvalidGenomicCoordsException
 * @throws InvalidColourException
 */
public String getChromIdeogram(int nDist, boolean noFormat) throws InvalidGenomicCoordsException, IOException, InvalidColourException {
    if (this.samSeqDict == null || this.samSeqDict.size() == 0) {
        return null;
    }
    List<Double> positionMap = null;
    try {
        positionMap = Utils.seqFromToLenOut(1, this.samSeqDict.getSequence(this.chrom).getSequenceLength(), this.getUserWindowSize());
    } catch (NullPointerException e) {
        throw new InvalidGenomicCoordsException();
    }
    // This code taken from printableRuler() above.
    String numberLine = "";
    int prevLen = 0;
    int j = 0;
    while (j < positionMap.size()) {
        int num = (int) Math.rint(Utils.roundToSignificantFigures(positionMap.get(j), 2));
        // String.valueOf(num);
        String posMark = Utils.parseIntToMetricSuffix(num);
        if (j == 0) {
            numberLine = posMark;
            j += posMark.length();
        } else if ((numberLine.length() - prevLen) >= nDist) {
            prevLen = numberLine.length();
            numberLine = numberLine + posMark;
            j += posMark.length();
        } else {
            numberLine = numberLine + SPACER;
            j++;
        }
    }
    List<String> map = new ArrayList<String>();
    for (int i = 0; i < numberLine.length(); i++) {
        map.add(numberLine.charAt(i) + "");
    }
    // ------------------
    int fromTextPos = Utils.getIndexOfclosestValue(this.from, positionMap);
    int toTextPos = Utils.getIndexOfclosestValue(this.to, positionMap);
    boolean isFirst = true;
    int lastTick = -1;
    for (int i = fromTextPos; i <= toTextPos; i++) {
        if (isFirst || map.get(i).equals(SPACER)) {
            map.set(i, TICKED);
            isFirst = false;
        }
        lastTick = i;
    }
    map.set(lastTick, TICKED);
    String ideogram = StringUtils.join(map, "");
    if (ideogram.length() > this.getUserWindowSize()) {
        ideogram = ideogram.substring(0, this.getUserWindowSize());
    }
    if (!noFormat) {
        ideogram = "\033[48;5;" + Config.get256Color(ConfigKey.background) + ";38;5;" + Config.get256Color(ConfigKey.chrom_ideogram) + "m" + ideogram;
    }
    return ideogram;
}

Example 3 with InvalidGenomicCoordsException

use of exceptions.InvalidGenomicCoordsException in project ASCIIGenome by dariober.

the class InteractiveInput method setGenome.

private void setGenome(List<String> cmdTokens, TrackProcessor proc) throws InvalidGenomicCoordsException, IOException, InvalidCommandLineException {
    List<String> tokens = new ArrayList<String>(cmdTokens);
    tokens.remove(0);
    if (tokens.size() == 0) {
        // Try to read fasta from history file
        ASCIIGenomeHistory ag = new ASCIIGenomeHistory();
        try {
            tokens.add(ag.getReference().get(0));
            System.err.println("Using " + ag.getReference().get(0));
        } catch (Exception e) {
            System.err.println("A previous reference file was not found.");
            throw new InvalidCommandLineException();
        }
    }
    GenomicCoords testSeqDict = new GenomicCoords("default", Utils.getTerminalWidth(), null, null);
    testSeqDict.setGenome(tokens, true);
    if (testSeqDict.getSamSeqDict() != null) {
        proc.getGenomicCoordsHistory().setGenome(tokens);
    } else {
        System.err.println(Utils.padEndMultiLine("Cannot set genome from " + tokens, Utils.getTerminalWidth()));
        this.interactiveInputExitCode = ExitCode.ERROR;
    }
}

Example 4 with InvalidGenomicCoordsException

use of exceptions.InvalidGenomicCoordsException in project ASCIIGenome by dariober.

the class TrackSet method addIntervalFeatureTrackFromVCF.

private void addIntervalFeatureTrackFromVCF(String sourceName, GenomicCoords gc, String trackTag) throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException {
    int idForTrack = this.getNextTrackId();
    // String trackId= new File(sourceName).getName() + "#" + idForTrack;
    String trackId = sourceName + "#" + idForTrack;
    // If this VCF file has sequence dictionary, check the coordinates in gc are compatible
    // If they are not, throw an exception which force resetting the coords.
    SAMSequenceDictionary seqDict = Utils.getVCFHeader(sourceName).getSequenceDictionary();
    if (seqDict != null && seqDict.getSequence(gc.getChrom()) == null) {
        throw new InvalidGenomicCoordsException();
    }
    TrackIntervalFeature tif = new TrackIntervalFeature(sourceName, gc);
    tif.setTrackTag(trackId);
    this.trackList.add(tif);
}

Example 5 with InvalidGenomicCoordsException

use of exceptions.InvalidGenomicCoordsException in project ASCIIGenome by dariober.

the class UcscGenePred method getCDS.

private List<IntervalFeature> getCDS(List<IntervalFeature> exons, final int cdsStart, final int cdsEnd, String cdsStartStat, String cdsEndStat) throws InvalidGenomicCoordsException {
    if (cdsStart > cdsEnd) {
        // There are no CDS in this transcript
        return new ArrayList<IntervalFeature>();
    }
    // Iterate through exons checking whether at least part of it is containing in the interval cdsStart:cdsEnd.
    // If so, take the exon slice inside the interval cdsStart:cdsEnd and add it to the list of CDSs
    List<IntervalFeature> cds = new ArrayList<IntervalFeature>();
    for (int i = 0; i < exons.size(); i++) {
        IntervalFeature exon = exons.get(i);
        if (exon.getTo() < cdsStart || exon.getFrom() > cdsEnd) {
            // Exon is not in interval cdsStart:cdsEnd
            continue;
        }
        int cdsFrom = exon.getFrom();
        if (cdsFrom < cdsStart) {
            // If only part of exon is CDS
            cdsFrom = cdsStart;
        }
        int cdsTo = exon.getTo();
        if (cdsTo > cdsEnd) {
            // If only part of exon is CDS
            cdsTo = cdsEnd;
        }
        String attr = Lists.newArrayList(Splitter.on("\t").omitEmptyStrings().split(exon.getRaw())).get(8);
        // Build the interval feature object
        String[] gff = new String[9];
        gff[0] = exons.get(0).getChrom();
        gff[1] = exons.get(0).getSource();
        gff[2] = "CDS";
        gff[3] = Integer.toString(cdsFrom);
        gff[4] = Integer.toString(cdsTo);
        gff[5] = ".";
        gff[6] = String.valueOf(exons.get(0).getStrand());
        // It's unclear to me how frames are assigned so leave it N/A.
        gff[7] = ".";
        gff[8] = attr;
        IntervalFeature x = new IntervalFeature(Joiner.on("\t").join(gff), TrackFormat.GTF, null);
        cds.add(x);
    }
    // and remove the remainder from the following CDS.
    if (exons.get(0).getStrand() == '+' && cdsEndStat.equals("cmpl")) {
        IntervalFeature stopCds = cds.get(cds.size() - 1);
        int newStop = stopCds.getTo() - 3;
        int remainder = -(newStop - stopCds.getFrom());
        if (remainder > 0) {
            // If remainder is > 0, this CDS doesn't exist at all and must be removed. This happens if the
            // stop codon is split across two exons (rare but it happens).
            // We also need to chip off "remainder" from the previous CDS.
            cds.remove(stopCds);
            stopCds = cds.get(cds.size() - 1);
            // I'm not sure why you need +1 to make it work!
            newStop = stopCds.getTo() - remainder + 1;
        }
        if (newStop <= 0 || newStop < stopCds.getFrom()) {
            // Sanity check
            throw new InvalidGenomicCoordsException();
        }
        // We create an intervalFeature from scratch that will replace the old one.
        List<String> raw = Lists.newArrayList(Splitter.on("\t").omitEmptyStrings().splitToList(stopCds.getRaw()));
        // Replace end coord
        raw.set(4, Integer.toString(newStop));
        // Replace last element.
        cds.set(cds.size() - 1, new IntervalFeature(Joiner.on("\t").join(raw), TrackFormat.GTF, null));
    } else if (exons.get(0).getStrand() == '-' && cdsStartStat.equals("cmpl")) {
        // same as above. This time apply to first CDS whose start has to be increased by 3
        IntervalFeature stopCds = cds.get(0);
        int newStop = stopCds.getFrom() + 3;
        int remainder = newStop - stopCds.getTo();
        if (remainder > 0) {
            // If remainder is >= 0, this CDS doesn't exist at all and must be removed. This happens if the
            // stop codon is split across two exons (rare but it happens).
            // We also need to chip off "remainder" from the next CDS.
            cds.remove(stopCds);
            stopCds = cds.get(0);
            // Not sure why -1 works!
            newStop = stopCds.getFrom() + remainder - 1;
        }
        if (newStop <= 0 || newStop > stopCds.getTo()) {
            // Sanity check
            throw new InvalidGenomicCoordsException();
        }
        // We create an intervalFeature from scratch that will replace the old one.
        List<String> raw = Lists.newArrayList(Splitter.on("\t").omitEmptyStrings().splitToList(stopCds.getRaw()));
        // Replace start coord
        raw.set(3, Integer.toString(newStop));
        // Replace last element.
        cds.set(0, new IntervalFeature(Joiner.on("\t").join(raw), TrackFormat.GTF, null));
    }
    return cds;
}