public void testReadPredictionXML() throws IOException {
String in = "testData/musite-test.pred.xml";
String out = in + ".gz";
PredictionResultXMLReader reader = PredictionResultXMLReader.createReader();
PredictionResult result = MusiteIOUtil.read(reader, in);
PredictionResultXMLWriter writer = PredictionResultXMLWriter.createWriter();
MusiteIOUtil.write(writer, out, result);
new File(out).delete();
}
public void testReadMusiteXML() throws IOException {
String xml = "testData/musite-test.xml";
String out = xml + ".gz";
ProteinsXMLReader reader = ProteinsXMLReader.createReader();
Proteins proteins = MusiteIOUtil.read(reader, xml);
System.out.println(proteins.proteinCount());
ProteinsXMLWriter writer = ProteinsXMLWriter.createWriter();
MusiteIOUtil.write(writer, out, proteins);
new File(out).delete();
}
public void testReadUniprotXML() throws IOException {
String xml = "testData/uniprot-test.xml";
String out = xml + ".tmp";
UniProtXMLReader reader = new UniProtXMLReader();
reader.setPTMFilter(PTM.PHOSPHORYLATION);
Proteins proteins = MusiteIOUtil.read(reader, xml);
System.out.println(proteins.proteinCount());
ProteinsXMLWriter writer = ProteinsXMLWriter.createWriter();
MusiteIOUtil.write(writer, out, proteins);
new File(out).delete();
}