public void importData() throws IOException, DaoException {
MySQLbulkLoader.bulkLoadOn();
FileReader reader = new FileReader(geneFile);
BufferedReader buf = new BufferedReader(reader);
String line = buf.readLine();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
while (line != null) {
if (pMonitor != null) {
pMonitor.incrementCurValue();
ConsoleUtil.showProgress(pMonitor);
}
if (!line.startsWith("#")) {
String parts[] = line.split("\t");
int entrezGeneId = Integer.parseInt(parts[1]);
String geneSymbol = parts[2];
Set<String> aliases;
if (parts[4].equals("-")) {
aliases = Collections.emptySet();
} else {
aliases = new HashSet<String>(Arrays.asList(parts[4].split("\\|")));
}
CanonicalGene gene = new CanonicalGene(entrezGeneId, geneSymbol, aliases);
daoGene.addGene(gene);
}
line = buf.readLine();
}
if (MySQLbulkLoader.isBulkLoad()) {
daoGene.flushGenesToDatabase();
}
}
public static void main(String[] args) throws Exception {
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
daoGene.deleteAllRecords();
if (args.length == 0) {
System.out.println("command line usage: importGenes.pl <ncbi_genes.txt>");
System.exit(1);
}
ProgressMonitor pMonitor = new ProgressMonitor();
pMonitor.setConsoleMode(true);
File geneFile = new File(args[0]);
System.out.println("Reading data from: " + geneFile.getAbsolutePath());
int numLines = FileUtil.getNumLines(geneFile);
System.out.println(" --> total number of lines: " + numLines);
pMonitor.setMaxValue(numLines);
ImportGeneData parser = new ImportGeneData(geneFile, pMonitor);
parser.importData();
ConsoleUtil.showWarnings(pMonitor);
System.err.println("Done.");
}