Examples with InvalidCommandLineException exceptions.InvalidCommandLineException used on opensource projects

Example 16 with InvalidCommandLineException

use of exceptions.InvalidCommandLineException in project ASCIIGenome by dariober.

the class TrackSet method replaceAwkFuncs.

/**
 *Replace in awk script the overloaded function name(s) with the actual names and args
 * @throws InvalidCommandLineException
 */
private String replaceAwkFuncs(String awkScript, Track track) throws InvalidCommandLineException {
    // Function name to be replaced
    final String FUNC = "get";
    // Search for 'foo FUNC(...) bar'. Use parenthesis to get the group "FUNC(...)".
    Pattern pattern = Pattern.compile(".*(" + FUNC + "\\(.+?\\)).*");
    while (awkScript.matches(".*\\b" + FUNC + "\\(.*")) {
        Matcher m = pattern.matcher(awkScript);
        m.matches();
        // this looks like "get(DP, 1, 2)"
        String func = m.group(1);
        int gapStart = m.start(1);
        int gapEnd = m.start(1) + func.length();
        // Remove func name and brackets, leave only param list. E.g. ["DP", "1", "2"]
        String xargs = func.replaceAll(".*\\(", "").replaceAll("\\).*", "");
        List<String> args = new ArrayList<String>();
        args.addAll(Splitter.on(",").splitToList(xargs));
        // Get the first arg i.e., the tag name, possibly in double quotes.
        String tag = args.get(0).replaceAll(".*\\(", "").replaceAll("\\).*", "").trim().replaceAll("^\"", "").replaceAll("\"$", "");
        // Depending on track type and tag we decide what the replacement function is
        String fname;
        if (track.getTrackFormat().equals(TrackFormat.BAM)) {
            fname = "getSamTag";
        } else if (track.getTrackFormat().equals(TrackFormat.VCF)) {
            if (tag.trim().startsWith("FMT/") || track.getVcfHeader().getFormatHeaderLine(tag) != null) {
                fname = "getFmtTag";
            } else if (tag.trim().startsWith("INFO/") || track.getVcfHeader().getInfoHeaderLine(tag) != null) {
                fname = "getInfoTag";
            } else {
                System.err.println("Tag " + tag + " not found in VCF header of track " + track.getTrackTag() + ".\n" + "Please prepend 'INFO/' or 'FMT/' to the tag to search the INFO or FORMAT fields, respectively.");
                throw new InvalidCommandLineException();
            }
        } else if (track.getTrackFormat().equals(TrackFormat.GTF)) {
            fname = "getGtfTag";
        } else if (track.getTrackFormat().equals(TrackFormat.GFF)) {
            fname = "getGffTag";
        } else {
            System.err.println("Function " + FUNC + " is not available for track type " + track.getTrackFormat() + ".");
            throw new InvalidCommandLineException();
        }
        args.set(0, '"' + tag + '"');
        func = fname + "(" + Joiner.on(",").join(args) + ")";
        awkScript = awkScript.substring(0, gapStart) + func + awkScript.substring(gapEnd, awkScript.length());
    }
    return awkScript;
}

Example 17 with InvalidCommandLineException

use of exceptions.InvalidCommandLineException in project ASCIIGenome by dariober.

the class UcscFetch method executeGenePredToGtf.

private File executeGenePredToGtf(File genePredToGtfExec, String dbNameTableName) throws InvalidCommandLineException, IOException, InterruptedException {
    List<String> args = parseCmdArgs(dbNameTableName);
    this.db = args.get(0);
    this.table = args.get(1);
    File outgtf = new File(tmpdir.getAbsolutePath(), this.db + ":" + this.table + ".gtf");
    outgtf.deleteOnExit();
    ProcessBuilder probuilder = new ProcessBuilder(genePredToGtfExec.getAbsolutePath(), "-utr", db, table, outgtf.getAbsolutePath());
    System.err.println("Querying UCSC...");
    // System.err.println(Joiner.on(" ").join(probuilder.command()));
    Process process = probuilder.start();
    process.waitFor();
    if (process.exitValue() != 0) {
        // System.err.println(Joiner.on(" ").join(probuilder.command()));
        throw new InvalidCommandLineException();
    }
    return outgtf;
}

Example 18 with InvalidCommandLineException

use of exceptions.InvalidCommandLineException in project ASCIIGenome by dariober.

the class TrackSetTest method canSetAwkForTrackIntervalFeature.

@Test
public void canSetAwkForTrackIntervalFeature() throws InvalidCommandLineException, IOException, InvalidGenomicCoordsException, ClassNotFoundException, InvalidRecordException, SQLException {
    TrackSet ts = new TrackSet();
    GenomicCoords gc = new GenomicCoords("chr1:1-100", 80, null, null);
    Track t1 = new TrackIntervalFeature("test_data/hg19_genes_head.gtf", gc);
    ts.addTrack(t1, "x");
    Track t2 = new TrackIntervalFeature("test_data/hg19_genes_head.gtf.gz", gc);
    ts.addTrack(t2, "x");
    Track t3 = new TrackIntervalFeature("test_data/refSeq.bed", gc);
    ts.addTrack(t3, "x");
    // Set for one track
    String cmdInput = "awk   '$3 == \"exon\"' #1";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    assertEquals("-F '\\t' '$3 == \"exon\"'", ts.getTrack(t1).getAwk());
    // As default
    assertEquals("", ts.getTrack(t3).getAwk());
    // Use custom delim, some tracks
    cmdInput = "awk -F _ '$3 == 10' #1 #3";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    assertEquals("-F _ '$3 == 10'", ts.getTrack(t1).getAwk());
    assertEquals("-F _ '$3 == 10'", ts.getTrack(t3).getAwk());
    // Use custom delim: All tracks
    cmdInput = "awk -v FOO=foo -F _ '$3 == 20'";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    assertEquals("-v FOO=foo -F _ '$3 == 20'", ts.getTrack(t1).getAwk());
    assertEquals("-v FOO=foo -F _ '$3 == 20'", ts.getTrack(t3).getAwk());
    // Turn off one track
    cmdInput = "awk -off #2";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    assertEquals("", ts.getTrack(t2).getAwk());
    // Turn off all tracks
    cmdInput = "awk";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    assertEquals("", ts.getTrack(t1).getAwk());
    assertEquals("", ts.getTrack(t2).getAwk());
    assertEquals("", ts.getTrack(t3).getAwk());
    // Invalid function
    cmdInput = "awk getSamTag()";
    boolean pass = false;
    try {
        ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    } catch (InvalidCommandLineException e) {
        pass = true;
    }
    assertTrue(pass);
    cmdInput = "awk getInfoTag()";
    pass = false;
    try {
        ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
    } catch (InvalidCommandLineException e) {
        pass = true;
    }
    assertTrue(pass);
    Track t4 = new TrackWiggles("test_data/ear045.oxBS.actb.tdf", gc, 4);
    ts.addTrack(t4, "x");
    cmdInput = "awk '1<2'";
    ts.setAwkForTrack(Utils.tokenize(cmdInput, " "));
}