/** @param args */
public static void main(String[] args) {
initOptions();
try {
parse(args, false);
String comm = args[1];
String buildOption = null;
// no needed to check as 'build' arg is required in Options
if (!commandLine.hasOption("build") || commandLine.getOptionValue("build").equals("")) {}
buildOption = commandLine.getOptionValue("build");
if (buildOption.equals("genome-sequence")) {
System.out.println("In genome-sequence");
String indir = commandLine.getOptionValue("indir");
String outfile = commandLine.getOptionValue("outfile", "/tmp/genome_sequence.json");
if (indir != null) {
GenomeSequenceFastaParser genomeSequenceFastaParser = new GenomeSequenceFastaParser();
genomeSequenceFastaParser.parseFastaGzipFilesToJson(new File(indir), new File(outfile));
}
}
if (buildOption.equals("core")) {
System.out.println("In core");
String gtfFile = commandLine.getOptionValue("gtf-file");
String geneDescriptionFile = commandLine.getOptionValue("gene-description", "");
String xrefFile = commandLine.getOptionValue("xref-file", "");
String tfbsFile = commandLine.getOptionValue("tfbs-file", "");
String mirnaFile = commandLine.getOptionValue("mirna-file", "");
String genomeSequenceDir = commandLine.getOptionValue("genome-sequence-dir", "");
String outfile = commandLine.getOptionValue("outfile", "/tmp/gene.json");
if (gtfFile != null) {
try {
GeneParser geneParser = new GeneParser();
geneParser.parse(
new File(gtfFile),
new File(geneDescriptionFile),
new File(xrefFile),
new File(tfbsFile),
new File(mirnaFile),
new File(genomeSequenceDir),
new File(outfile));
} catch (SecurityException | NoSuchMethodException | FileFormatException e) {
e.printStackTrace();
}
}
}
if (buildOption.equals("variation")) {
System.out.println("In variation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
System.out.println("chunksize: " + chunksize);
String outfile = commandLine.getOptionValue("outfile", "/tmp/variation.json");
if (indir != null) {
VariationParser vp = new VariationParser();
vp.createVariationDatabase(Paths.get(indir));
vp.connect(Paths.get(indir));
// List<String> res = vp.queryByVariationId(13, "variation_synonym",
// Paths.get(indir));
// System.out.println("a");
// res = vp.queryByVariationId(4, "variation_synonym", Paths.get(indir));
// System.out.println("b");
// res = vp.queryByVariationId(8, "variation_synonym", Paths.get(indir));
// System.out.println("c");
vp.parseVariationToJson("", "", "", "", Paths.get(indir), Paths.get(outfile));
vp.disconnect();
}
}
if (buildOption.equals("regulation")) {
System.out.println("In regulation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
System.out.println("chunksize: " + chunksize);
String outfile = commandLine.getOptionValue("outfile", "/tmp/regulations.json");
if (indir != null) {
try {
RegulatoryParser.parseRegulatoryGzipFilesToJson(
Paths.get(indir), chunksize, Paths.get(outfile));
} catch (ClassNotFoundException | NoSuchMethodException | SQLException e) {
e.printStackTrace();
}
}
}
if (buildOption.equals("conservation")) {
System.out.println("In conservation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
String outfile = commandLine.getOptionValue("outfile", "/tmp/conservation.json");
if (indir != null) {
ConservedRegionParser.parseConservedRegionFilesToJson(
Paths.get(indir), chunksize, Paths.get(outfile));
}
}
} catch (ParseException | IOException | SQLException | ClassNotFoundException e) {
e.printStackTrace();
}
}
