public static void main(String[] args) {
File inputFile =
args.length > 0
? new File(args[0])
: new File("C:\\Documents and Settings\\tdanford\\Desktop\\sacCer1.gff");
try {
SGDGFFParser parser = new SGDGFFParser();
BinCalculator bincalc = new BinCalculator();
parser.parseInputFile(inputFile);
for (String k : parser.geneFeatures.keySet()) {
try {
GeneFeatures gf = parser.geneFeatures.get(k);
StringBuffer line = new StringBuffer();
ArrayList<Integer> starts = new ArrayList<Integer>();
ArrayList<Integer> ends = new ArrayList<Integer>();
for (GFFRecord cds : gf.cds) {
starts.add(cds.getStart());
ends.add(cds.getEnd());
}
if (starts.size() == 0) {
starts.add(gf.gene.getStart());
ends.add(gf.gene.getEnd());
}
Collections.sort(starts);
Collections.sort(ends);
String strand = "";
if (gf.gene.getStrand() == StrandedFeature.NEGATIVE) {
strand = "-";
} else if (gf.gene.getStrand() == StrandedFeature.POSITIVE) {
strand = "+";
}
/* dumb that we have to put this back on, but that's the UCSC standard format */
String chrom = "chr" + Genome.fixYeastChrom(gf.gene.getSeqName());
line.append(gf.id + "\t");
line.append(chrom + "\t"); // do we need to get rid of roman numerals here ?
line.append(strand + "\t");
line.append(gf.gene.getStart() + "\t");
line.append(gf.gene.getEnd() + "\t");
line.append(starts.get(0) + "\t");
line.append(ends.get(ends.size() - 1) + "\t");
line.append(starts.size() + "\t");
for (int i = 0; i < starts.size(); i++) {
if (i == 0) {
line.append(starts.get(i));
} else {
line.append("," + starts.get(i));
}
}
line.append("\t");
for (int i = 0; i < ends.size(); i++) {
if (i == 0) {
line.append(ends.get(i));
} else {
line.append("," + ends.get(i));
}
}
line.append("\t");
// no protein ID
System.out.println(line);
} catch (Exception e) {
System.err.println(e.toString());
e.printStackTrace();
}
}
for (GFFRecord record : parser.otherRecords) {
if (record.getFeature().equals("intron")) {
continue;
}
try {
StringBuffer line = new StringBuffer();
line.append(bincalc.getBinFromRange(record.getStart(), record.getEnd()) + "\t");
String strand = "";
if (record.getStrand() == StrandedFeature.NEGATIVE) {
strand = "-";
} else if (record.getStrand() == StrandedFeature.POSITIVE) {
strand = "+";
}
/* dumb that we have to put this back on, but that's the UCSC standard format */
String chrom = "chr" + Genome.fixYeastChrom(record.getSeqName());
Map<String, List<String>> attrs = decodeAttrMap(record);
String name = "";
if (attrs != null && attrs.containsKey("Name") && attrs.get("Name").size() > 0) {
name = attrs.get("Name").get(0);
} else if (attrs != null && attrs.containsKey("ID") && attrs.get("ID").size() > 0) {
name = attrs.get("ID").get(0);
}
line.append(chrom + "\t");
line.append(record.getStart() + "\t" + record.getEnd() + "\t");
line.append(name + "\t");
line.append(record.getScore() + "\t");
line.append(strand + "\t");
line.append(record.getFeature());
System.out.println(line);
} catch (Exception e) {
System.err.println(e.toString());
e.printStackTrace();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}