public void parseInputFile(File inputFile) throws IOException {
geneFeatures.clear();
otherRecords.clear();
try {
GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);
Iterator itr = gffEntries.lineIterator();
int count = 0;
int intronFeatures = 0;
LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();
while (itr.hasNext()) {
Object val = itr.next();
if (val instanceof GFFRecord) {
GFFRecord rec = (GFFRecord) val;
count += 1;
if (rec.getFeature().endsWith("gene")) {
GeneFeatures gf = new GeneFeatures(rec);
geneFeatures.put(gf.id, gf);
} else if (rec.getFeature().equals("CDS")) {
cdsRecs.addLast(rec);
} else {
otherRecords.add(rec);
}
}
}
for (GFFRecord rec : cdsRecs) {
Map<String, List<String>> attrs = decodeAttrMap(rec);
if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
} else {
System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
}
}
for (String k : geneFeatures.keySet()) {
GeneFeatures gf = geneFeatures.get(k);
if (gf.cds != null && gf.cds.size() > 1) {
intronFeatures++;
}
}
System.err.println("# GFF Records: " + count);
System.err.println("# Gene Feature Sets: " + geneFeatures.size());
System.err.println("\t# Intron-Features: " + intronFeatures);
} catch (ParserException e) {
e.printStackTrace();
} catch (BioException e) {
e.printStackTrace();
}
}
public static Map<String, List<String>> decodeAttrMap(GFFRecord rec) {
Map<String, List<String>> map = new HashMap<String, List<String>>();
for (Object ko : rec.getGroupAttributes().keySet()) {
String str = (String) ko;
Pair<String, List<String>> vals = decodeKeyValues(str);
if (vals != null) {
map.put(vals.getFirst(), vals.getLast());
}
}
return map;
}
public GeneFeatures(GFFRecord g) {
if (!g.getFeature().endsWith("gene")) {
throw new IllegalArgumentException();
}
gene = g;
geneAttrs = decodeAttrMap(g);
cds = new LinkedList<GFFRecord>();
if (!geneAttrs.containsKey("ID")) {
throw new IllegalArgumentException();
}
id = geneAttrs.get("ID").get(0);
}
public void addCDS(GFFRecord rec, Map<String, List<String>> attrs) {
if (!rec.getFeature().equals("CDS")) {
throw new IllegalArgumentException();
}
if (attrs == null) {
attrs = decodeAttrMap(rec);
}
if (!attrs.containsKey("Parent")) {
throw new IllegalArgumentException();
}
if (!attrs.get("Parent").contains(id)) {
throw new IllegalArgumentException();
}
cds.addLast(rec);
}
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();
}
}