public void addPredictedGene(PredictedGene gene) {
root.addContent(gene.asJDomElement());
}
public static void main(String[] args) {
if (args.length != 2) {
System.out.println(
"This program expects two parameters: \n"
+ "1. Input predicted genes XML filename \n"
+ "2. Output GFF filename\n");
} else {
String inFileString = args[0];
String outFileString = args[1];
File inFile = new File(inFileString);
File outFile = new File(outFileString);
try {
BufferedWriter outBuff = new BufferedWriter(new FileWriter(outFile));
// writing header first
outBuff.write(GFF_HEADER + "\n");
Date currentDate = new Date();
outBuff.write(DATE_HEADER + currentDate.toString() + "\n");
outBuff.write(TYPE_HEADER + "\n");
BufferedReader reader = new BufferedReader(new FileReader(inFile));
String tempSt;
StringBuilder stBuilder = new StringBuilder();
while ((tempSt = reader.readLine()) != null) {
stBuilder.append(tempSt);
}
// closing input file reader
reader.close();
Annotation annotation = new Annotation(stBuilder.toString());
HashMap<String, TreeSet<GffLine>> linesPerContig = new HashMap<String, TreeSet<GffLine>>();
// -----------POTATIZING GENES----------------
List<Element> contigsGenes =
annotation
.asJDomElement()
.getChild(PredictedGenes.TAG_NAME)
.getChildren(ContigXML.TAG_NAME);
for (Element element : contigsGenes) {
ContigXML contig = new ContigXML(element);
TreeSet<GffLine> lines = new TreeSet<GffLine>();
linesPerContig.put(contig.getId(), lines);
List<XMLElement> genes = contig.getChildrenWith(PredictedGene.TAG_NAME);
for (XMLElement xMLElement : genes) {
PredictedGene gene = new PredictedGene(xMLElement.asJDomElement());
String geneLine =
contig.getId() + SEPARATOR + CHORIZO_GEN + SEPARATOR + GENE + SEPARATOR;
int beginPos = gene.getStartPosition();
int endPos = gene.getEndPosition();
int initPos = beginPos;
if (beginPos < endPos) {
geneLine += beginPos + SEPARATOR + endPos + SEPARATOR;
} else {
geneLine += endPos + SEPARATOR + beginPos + SEPARATOR;
initPos = endPos;
}
geneLine +=
gene.getEvalue()
+ SEPARATOR
+ gene.getStrand()
+ SEPARATOR
+ "."
+ SEPARATOR
+ LOCUS_TAG
+ gene.getId()
+ ";\n";
lines.add(new GffLine(initPos, geneLine));
// outBuff.write(geneLine);
String cdsLine = contig.getId() + SEPARATOR + CHORIZO_GEN + SEPARATOR + CDS + SEPARATOR;
if (gene.getStrand().equals(PredictedGene.POSITIVE_STRAND)) {
cdsLine +=
gene.getStartPosition() + SEPARATOR + (gene.getEndPosition() - 3) + SEPARATOR;
} else {
cdsLine +=
(gene.getEndPosition() - 3) + SEPARATOR + gene.getStartPosition() + SEPARATOR;
}
cdsLine +=
gene.getEvalue() + SEPARATOR + gene.getStrand() + SEPARATOR + "0" + SEPARATOR;
cdsLine +=
LOCUS_TAG
+ gene.getId()
+ ";"
+ PRODUCT
+ gene.getProteinNames()
+ ";"
+ CHORIZO_INFERENCE
+ gene.getAccession()
+ "\n";
// outBuff.write(cdsLine);
lines.add(new GffLine(initPos, cdsLine));
String startCodonLine =
contig.getId() + SEPARATOR + CHORIZO_GEN + SEPARATOR + START_CODON + SEPARATOR;
if (gene.getStrand().equals(PredictedGene.POSITIVE_STRAND)) {
startCodonLine +=
gene.getStartPosition() + SEPARATOR + (gene.getStartPosition() + 2) + SEPARATOR;
} else {
startCodonLine +=
(gene.getStartPosition() - 2) + SEPARATOR + gene.getStartPosition() + SEPARATOR;
}
startCodonLine +=
gene.getEvalue()
+ SEPARATOR
+ gene.getStrand()
+ SEPARATOR
+ "0"
+ SEPARATOR
+ LOCUS_TAG
+ gene.getId()
+ ";";
startCodonLine +=
PRODUCT
+ gene.getProteinNames()
+ ";"
+ CHORIZO_INFERENCE
+ gene.getAccession()
+ "\n";
// outBuff.write(startCodonLine);
lines.add(new GffLine(initPos, startCodonLine));
String stopCodonLine =
contig.getId() + SEPARATOR + CHORIZO_GEN + SEPARATOR + STOP_CODON + SEPARATOR;
if (gene.getStrand().equals(PredictedGene.POSITIVE_STRAND)) {
stopCodonLine +=
(gene.getEndPosition() + 1) + SEPARATOR + (gene.getEndPosition() + 3) + SEPARATOR;
} else {
stopCodonLine +=
(gene.getEndPosition() - 3) + SEPARATOR + (gene.getEndPosition() - 1) + SEPARATOR;
}
stopCodonLine +=
gene.getEvalue()
+ SEPARATOR
+ gene.getStrand()
+ SEPARATOR
+ "0"
+ SEPARATOR
+ LOCUS_TAG
+ gene.getId()
+ ";";
stopCodonLine +=
PRODUCT
+ gene.getProteinNames()
+ ";"
+ CHORIZO_INFERENCE
+ gene.getAccession()
+ "\n";
// outBuff.write(stopCodonLine);
lines.add(new GffLine(initPos, stopCodonLine));
}
}
// -----------POTATIZING RNAS-----------------
List<Element> contigsRnas =
annotation
.asJDomElement()
.getChild(PredictedRnas.TAG_NAME)
.getChildren(ContigXML.TAG_NAME);
for (Element element : contigsRnas) {
ContigXML contig = new ContigXML(element);
List<XMLElement> rnas = contig.getChildrenWith(PredictedRna.TAG_NAME);
TreeSet<GffLine> lines = linesPerContig.get(contig.getId());
if (lines == null) {
lines = new TreeSet<GffLine>();
linesPerContig.put(contig.getId(), lines);
}
for (XMLElement xMLElement : rnas) {
PredictedRna rna = new PredictedRna(xMLElement.asJDomElement());
String rnaLine = contig.getId() + SEPARATOR + CHORIZO_RNA + SEPARATOR + RNA + SEPARATOR;
int beginPos = rna.getStartPosition();
int endPos = rna.getEndPosition();
int initPos = beginPos;
if (beginPos < endPos) {
rnaLine += beginPos + SEPARATOR + endPos + SEPARATOR;
} else {
rnaLine += endPos + SEPARATOR + beginPos + SEPARATOR;
initPos = endPos;
}
rnaLine +=
rna.getEvalue()
+ SEPARATOR
+ rna.getStrand()
+ SEPARATOR
+ "."
+ SEPARATOR
+ LOCUS_TAG
+ rna.getId()
+ ";";
String columns[] = rna.getAnnotationUniprotId().split("\\|");
String rnaProduct = columns[3];
String refSeqId = columns[1];
String positions = columns[2].substring(1);
// ref|NC_007413|:3894075-3895562|16S ribosomal RNA| [locus_tag=Ava_R0035]
rnaLine +=
PRODUCT + rnaProduct + "," + "rna:RefSeq:" + refSeqId + " " + positions + "\n";
// outBuff.write(rnaLine);
lines.add(new GffLine(initPos, rnaLine));
}
}
Set<String> keys = linesPerContig.keySet();
for (String key : keys) {
TreeSet<GffLine> lines = linesPerContig.get(key);
GffLine line = lines.pollFirst();
while (line != null) {
outBuff.write(line.getLine());
line = lines.pollFirst();
}
}
outBuff.close();
System.out.println("Done!!! :D");
} catch (Exception e) {
e.printStackTrace();
}
}
}