Examples with CharSplitter com.github.lindenb.jvarkit.lang.CharSplitter used on opensource projects

Example 26 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class VcfRenameSamples method parseNames.

private void parseNames(final Path f) throws IOException {
    final CharSplitter tab = CharSplitter.TAB;
    final BufferedReader in = IOUtils.openPathForBufferedReading(f);
    String line;
    while ((line = in.readLine()) != null) {
        if (line.startsWith("#"))
            continue;
        if (StringUtil.isBlank(line))
            continue;
        final String[] tokens = tab.split(line);
        if (tokens.length != 2)
            throw new IOException("Expected two columns in \"" + line + "\" : " + f);
        tokens[0] = tokens[0].trim();
        tokens[1] = tokens[1].trim();
        if (StringUtil.isBlank(tokens[0]))
            throw new IOException("Empty src-name in \"" + line + "\" : " + f);
        if (StringUtil.isBlank(tokens[1]))
            throw new IOException("Empty dest-name in \"" + line + "\" : " + f);
        if (tokens[0].equals(tokens[1])) {
            LOG.warning("Same src/dest in in \"" + line + "\" : " + f);
            continue;
        }
        if (this.oldNameToNewName.containsKey(tokens[0])) {
            final String dest = this.oldNameToNewName.get(tokens[0]);
            if (dest.equals(tokens[1])) {
                LOG.warning(tokens[0] + " -> " + tokens[1] + " defined twice");
                continue;
            } else {
                throw new IOException("Empty src-name was first defined as " + dest + " and now as " + tokens[1] + " in \"" + line + "\" : " + f);
            }
        }
        this.oldNameToNewName.put(tokens[0], tokens[1]);
    }
    in.close();
}

Example 27 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class BackLocate method run.

private void run(final PrintStream out, final BufferedReader in) throws IOException {
    final CharSplitter tab = CharSplitter.TAB;
    String line;
    while ((line = in.readLine()) != null) {
        if (line.startsWith("#") || StringUtils.isBlank(line))
            continue;
        final String[] tokens = JvarkitException.TokenErrors.atLeast(2, tab.split(line, 3));
        final String geneName = tokens[0].trim();
        if (StringUtils.isBlank(geneName))
            throw new IOException("Bad line. No gene in " + geneName);
        final String mut = tokens[1].trim();
        int x0 = 0, x1 = 0;
        while (x1 < mut.length() && Character.isLetter(mut.charAt(x1))) {
            ++x1;
        }
        String substr = mut.substring(x0, x1);
        final AminoAcids.AminoAcid aa1 = substr.length() == 1 ? AminoAcids.getAminoAcidFromOneLetterCode(substr.charAt(0)) : AminoAcids.getAminoAcidFromThreeLettersCode(substr);
        if (aa1 == null)
            throw new JvarkitException.UserError("Bad mutation " + mut + " (cannot parse left AA)");
        x0 = x1;
        while (x1 < mut.length() && Character.isDigit(mut.charAt(x1))) {
            ++x1;
        }
        substr = mut.substring(x0, x1);
        if (!StringUtils.isInteger(substr))
            throw new JvarkitException.UserError("Bad mutation " + mut + " (cannot parse position)");
        final int position1 = Integer.parseInt(substr);
        if (position1 == 0)
            throw new IOException("Bad position in protein (" + substr + ") in " + line);
        substr = mut.substring(x1);
        final AminoAcids.AminoAcid aa2 = substr.length() == 1 ? AminoAcids.getAminoAcidFromOneLetterCode(substr.charAt(0)) : AminoAcids.getAminoAcidFromThreeLettersCode(substr);
        if (aa2 == null)
            throw new JvarkitException.UserError("Bad mutation " + mut + " (cannot parse right AA)");
        final List<Transcript> transcripts = this.name2transcripts.get(geneName.toUpperCase());
        if (transcripts == null || transcripts.isEmpty()) {
            LOG.warn("no transcript found for " + geneName);
            continue;
        }
        for (final Transcript transcript : transcripts) {
            backLocate(out, transcript, geneName, aa1, aa2, position1, tokens.length > 2 ? tokens[2] : ".");
        }
    }
}

Example 28 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class Biostar214299 method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.positionFile == null) {
        LOG.error("position File is not defined.");
        return -1;
    }
    final String UNAFFECTED_SAMPLE = "UNAFFECTED";
    final String AMBIGOUS_SAMPLE = "AMBIGOUS";
    final String UNMAPPED = "UNMAPPED";
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    final IntervalTreeMap<Position> positionsTreeMap = new IntervalTreeMap<>();
    final Set<String> samples = new HashSet<>();
    try {
        sfr = openSamReader(oneFileOrNull(args));
        final SAMFileHeader header = sfr.getFileHeader();
        final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(header);
        try (BufferedReader br = IOUtils.openPathForBufferedReading(this.positionFile)) {
            String line;
            final CharSplitter tab = CharSplitter.TAB;
            while ((line = br.readLine()) != null) {
                if (StringUtils.isBlank(line) || line.startsWith("#"))
                    continue;
                final String[] tokens = tab.split(line);
                if (tokens.length < 4) {
                    LOG.error("Not enough columns in " + line);
                    return -1;
                }
                final String contig = tokens[0];
                if (dict.getSequence(contig) == null) {
                    LOG.error(JvarkitException.ContigNotFoundInDictionary.getMessage(contig, dict));
                    return -1;
                }
                final int refpos = Integer.parseInt(tokens[1]);
                final Interval interval = new Interval(contig, refpos, refpos);
                Position position = positionsTreeMap.get(interval);
                if (position == null) {
                    position = new Position();
                    // position.contig = contig;
                    position.refpos = refpos;
                    positionsTreeMap.put(interval, position);
                }
                final String bases = tokens[2].toUpperCase();
                if (bases.length() != 1 || !bases.matches("[ATGC]")) {
                    LOG.error("in " + line + " bases should be one letter and ATGC");
                    return -1;
                }
                if (position.base2sample.containsKey(bases.charAt(0))) {
                    LOG.error("in " + line + " bases already defined for this position");
                    return -1;
                }
                final String sampleName = tokens[3].trim();
                if (sampleName.isEmpty()) {
                    LOG.error("sample name cannot be empty");
                    return -1;
                }
                samples.add(sampleName);
                position.base2sample.put(bases.charAt(0), sampleName);
            }
        } catch (final IOException err) {
            LOG.error(err);
            return -1;
        }
        if (samples.contains(UNAFFECTED_SAMPLE)) {
            LOG.error("Sample cannot be named " + UNAFFECTED_SAMPLE);
            return -1;
        }
        if (samples.contains(AMBIGOUS_SAMPLE)) {
            LOG.error("Sample cannot be named " + AMBIGOUS_SAMPLE);
            return -1;
        }
        if (samples.contains(UNMAPPED)) {
            LOG.error("Sample cannot be named " + UNMAPPED);
            return -1;
        }
        samples.add(UNAFFECTED_SAMPLE);
        samples.add(AMBIGOUS_SAMPLE);
        samples.add(UNMAPPED);
        final SAMFileHeader newHeader = new SAMFileHeader();
        newHeader.setSortOrder(header.getSortOrder());
        newHeader.setSequenceDictionary(dict);
        newHeader.addComment("generated with " + getProgramName() + " " + getVersion() + " Pierre Lindenbaum : " + getProgramCommandLine());
        /* create groups */
        for (final String sample : samples) {
            final SAMReadGroupRecord rg = new SAMReadGroupRecord(sample);
            rg.setSample(sample);
            rg.setLibrary(sample);
            newHeader.addReadGroup(rg);
        }
        sfw = this.writingBamArgs.setReferencePath(this.reference).openSamWriter(this.outputFile, newHeader, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header).logger(LOG);
        final SAMRecordIterator iter = sfr.iterator();
        while (iter.hasNext()) {
            final SAMRecord rec = progress.watch(iter.next());
            rec.setAttribute("RG", null);
            if (rec.getReadUnmappedFlag()) {
                rec.setAttribute("RG", UNMAPPED);
                sfw.addAlignment(rec);
                continue;
            }
            final Cigar cigar = rec.getCigar();
            final Collection<Position> snps = positionsTreeMap.getContained(new Interval(rec.getContig(), rec.getUnclippedStart(), rec.getUnclippedEnd()));
            if (snps == null || snps.isEmpty()) {
                rec.setAttribute("RG", UNAFFECTED_SAMPLE);
                sfw.addAlignment(rec);
                continue;
            }
            final Map<Integer, Position> index2pos = snps.stream().collect(Collectors.toMap(P -> P.refpos, P -> P));
            final Set<String> selectedSamples = new HashSet<>();
            final byte[] bases = rec.getReadBases();
            if (bases == null || bases.equals(SAMRecord.NULL_SEQUENCE)) {
                LOG.error("Bases missing in read " + rec);
                return -1;
            }
            int refPos1 = rec.getUnclippedStart();
            int readPos0 = 0;
            for (final CigarElement ce : cigar.getCigarElements()) {
                final CigarOperator op = ce.getOperator();
                final boolean consummeReadBaseOrSoftClip = op.consumesReadBases() || op.equals(CigarOperator.S);
                if (op.consumesReferenceBases() && consummeReadBaseOrSoftClip) {
                    for (int i = 0; i < ce.getLength(); ++i) {
                        final int nowRefPos1 = (refPos1 + i);
                        final int nowReadPos0 = (readPos0 + i);
                        final Position position = index2pos.get(nowRefPos1);
                        if (position == null)
                            continue;
                        if (nowReadPos0 >= bases.length)
                            continue;
                        final char base = (char) Character.toUpperCase(bases[nowReadPos0]);
                        final String sample = position.base2sample.get(base);
                        if (sample == null)
                            continue;
                        selectedSamples.add(sample);
                        index2pos.remove(nowRefPos1);
                        if (index2pos.isEmpty())
                            break;
                    }
                }
                if (op.consumesReferenceBases() || op.isClipping()) {
                    refPos1 += ce.getLength();
                }
                if (consummeReadBaseOrSoftClip) {
                    readPos0 += ce.getLength();
                }
            }
            if (selectedSamples.isEmpty()) {
                rec.setAttribute("RG", UNAFFECTED_SAMPLE);
            } else if (selectedSamples.size() == 1) {
                rec.setAttribute("RG", selectedSamples.iterator().next());
            } else {
                rec.setAttribute("RG", AMBIGOUS_SAMPLE);
            }
            sfw.addAlignment(rec);
        }
        progress.finish();
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}