private void run(VcfIterator in) {
for (; ; ) {
VariantContext ctx = null;
if (in.hasNext()) ctx = in.next();
if (ctx == null
|| this.genes.isEmpty()
|| (!this.genes.isEmpty() && !this.genes.get(0).getChr().equals(ctx.getChr()))
|| (!this.genes.isEmpty() && this.chromEnd <= ctx.getStart())) {
this.print();
if (System.out.checkError()) return;
if (ctx == null) return;
this.clear();
if (chrom2knownGenes.containsKey(ctx.getChr())) {
for (KnownGene g : chrom2knownGenes.get(ctx.getChr())) {
if (this.genes.isEmpty()) {
if (g.getTxEnd() <= ctx.getStart() || g.getTxStart() > ctx.getEnd()) {
continue;
}
this.addGene(g);
} else {
if (!(g.getTxStart() > this.chromEnd || g.getTxEnd() <= this.chromStart)) {
this.addGene(g);
}
}
}
if (genes.isEmpty()) {
debug("no gene for " + ctx.getChr() + ":" + ctx.getStart());
}
} else {
debug("not any gene for " + ctx.getChr());
}
}
if (!genes.isEmpty()
&& ctx.getStart() - 1 >= this.chromStart
&& ctx.getStart() <= this.chromEnd) {
this.addVariant(ctx);
}
}
}
private void print() {
if (this.positions.isEmpty()) {
return;
}
++count_pages_printed;
final KnownGene first = genes.get(0);
final double fHeight = 20;
final Dimension localPage =
new Dimension(
(int) (this.pageDef.width),
(int)
(margin.top
+ margin.bottom
+ (this.genes.size() + 1) * fHeight
+ this.sample2positions.size() * fHeight));
System.out.println("\n%%Page: " + count_pages_printed + " " + count_pages_printed);
System.out.println("gsave");
System.out.println(
1.0
+ " "
+ (localPage.height <= this.pageDef.height
? 1.0
: 1.0 / (localPage.getHeight() / (float) this.pageDef.getHeight()))
+ " scale");
// System.out.println( "%%BoundingBox: 0 0 " + page.width + " " + page.height );
float midy = (float) (fHeight / 2.0f);
double cdsHeight = fHeight * 0.4;
double exonHeight = fHeight * 0.9;
System.out.println(
"2 "
+ (localPage.height - 10)
+ " moveto ("
+ first.getChromosome()
+ ":"
+ this.chromStart
+ "-"
+ this.chromEnd
+ ") show");
System.out.println("1 0 0 setrgbcolor");
System.out.println("0.3 setlinewidth");
for (Integer r : this.positions) {
System.out.print(
"newpath "
+ (float) toPixel(r)
+ " 0 moveto 0 "
+ localPage.height
+ " rlineto stroke\n");
System.out.print(
(float) toPixel(r)
+ " "
+ (localPage.height - 5)
+ " moveto -90 rotate ("
+ (r)
+ ") show 90 rotate\n");
}
for (int i = 0; i < this.genes.size(); ++i) {
KnownGene g = this.genes.get(i);
System.out.println("gsave");
System.out.println("0 " + (localPage.height - margin.top - (fHeight * i)) + " translate");
double x1 = toPixel(g.getTxStart());
double x2 = toPixel(g.getTxEnd());
System.out.print("0 0 0 setrgbcolor\n");
NEWPATH();
MOVETO(x1, midy);
LINETO(x2, midy);
STROKE();
// draw ticks
System.out.print("0.2 setlinewidth\n");
System.out.print("newpath\n");
System.out.print(x1 + " " + midy + " moveto\n");
System.out.print(x1 + " " + x2 + (g.isPositiveStrand() ? " forticksF" : " forticksR") + "\n");
System.out.print("closepath stroke\n");
System.out.print("0.5 setlinewidth\n");
// draw txStart/txEnd
System.out.print(
"0.1 0.1 0.5 setrgbcolor\n"
+ "newpath\n"
+ +toPixel(g.getCdsStart())
+ " "
+ +(midy - cdsHeight / 2.0)
+ " "
+ (toPixel(g.getCdsEnd()) - toPixel(g.getCdsStart()))
+ " "
+ cdsHeight
+ " box closepath fill\n");
// draw each exon
for (int j = 0; j < g.getExonCount(); ++j) {
System.out.print(
toPixel(g.getExon(j).getStart())
+ " "
+ (midy - exonHeight / 2.0)
+ " "
+ (float) (toPixel(g.getExon(j).getEnd()) - toPixel(g.getExon(j).getStart()))
+ " "
+ exonHeight
+ " gradient\n");
}
// draw name
System.out.print("0 0 0 setrgbcolor\n");
System.out.print("10 " + midy + " moveto (" + g.getName() + ") show\n");
System.out.println("grestore");
}
// samples
{
double y = localPage.height - margin.top - (fHeight * (this.genes.size() + 1));
for (String sample : this.sample2positions.keySet()) {
System.out.print("0.2 setlinewidth\n");
System.out.print("0 0 0 setrgbcolor\n");
System.out.print("10 " + (y - midy + 5) + " moveto (" + sample + ") show\n");
System.out.print(
"newpath "
+ margin.left
+ " "
+ y
+ " moveto\n"
+ pageDef.width
+ " "
+ 0
+ " rlineto stroke\n");
for (Integer r2 : this.sample2positions.get(sample)) {
System.out.print("0.8 setlinewidth\n");
System.out.print("newpath " + toPixel(r2) + " " + y + " circle closepath stroke\n");
}
y -= fHeight;
}
}
System.out.println("grestore");
System.out.print("showpage\n");
}
private void addGene(KnownGene g) {
chromStart = Math.min(chromStart, g.getTxStart());
chromEnd = Math.max(chromEnd, g.getTxEnd());
genes.add(g);
}
@Override
public int doWork(String[] args) {
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "k:")) != -1) {
switch (c) {
case 'k':
this.ucscKnownGene = opt.getOptArg();
break;
default:
{
switch (handleOtherOptions(c, opt, null)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
VcfIterator iter = null;
BufferedReader r = null;
try {
if (opt.getOptInd() == args.length) {
info("Reading from stdin");
iter = new VcfIterator(System.in);
} else if (opt.getOptInd() + 1 == args.length) {
String uri = args[opt.getOptInd()];
info("Reading from " + uri);
iter = new VcfIterator(IOUtils.openURIForReading(uri));
} else {
error("Illegal number of arguments.");
return -1;
}
info("Reading " + this.ucscKnownGene);
SAMSequenceDictionary dict = iter.getHeader().getSequenceDictionary();
int nKG = 0;
r = IOUtils.openURIForBufferedReading(ucscKnownGene);
Pattern tab = Pattern.compile("[\t]");
String line;
while ((line = r.readLine()) != null) {
String tokens[] = tab.split(line);
KnownGene g = new KnownGene(tokens);
if (dict != null && dict.getSequence(g.getChr()) == null) continue;
List<KnownGene> kg = this.chrom2knownGenes.get(g.getChr());
if (kg == null) {
kg = new ArrayList<KnownGene>();
this.chrom2knownGenes.put(g.getChr(), kg);
}
kg.add(g);
++nKG;
}
r.close();
info("Done Reading knownGenes. N=" + nKG);
final double ticksH = (fHeight / 2.0f) * 0.6f;
final double ticksx = 20;
System.out.print(
"%!PS\n"
+ "%%Creator: Pierre Lindenbaum PhD [email protected] http://plindenbaum.blogspot.com\n"
+ "%%Title: "
+ getClass().getSimpleName()
+ "\n"
+ "%%CreationDate: "
+ new Date()
+ "\n"
+ "%%EndComments\n"
+ "%%BoundingBox: 0 0 "
+ (this.pageDef.width + margin.left + margin.right)
+ " "
+ (this.pageDef.height + margin.top + margin.bottom)
+ "\n"
+ "/Courier findfont 9 scalefont setfont\n"
+ "/circle { 10 0 360 arc} bind def\n"
+ "/ticksF {\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ ticksH
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ ticksH
+ " "
+ ticksH
+ " rmoveto\n"
+ "} bind def\n"
+ "/ticksR {\n"
+ (ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ "} bind def\n"
+ "/forticksF {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ "ticksF "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/forticksR {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ " ticksR "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/box\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "x y moveto\n"
+ "width 0 rlineto\n"
+ "0 height rlineto\n"
+ "width -1 mul 0 rlineto\n"
+ "0 height -1 mul rlineto\n"
+ "end\n"
+ "} bind def\n"
+ "/gradient\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "/i 0 def\n"
+ "height 2 div /i exch def\n"
+ "\n"
+ "0 1 height 2 div {\n"
+ " 1 i height 2.0 div div sub setgray\n"
+ " newpath\n"
+ " x \n"
+ " y height 2 div i sub add\n"
+ " width\n"
+ " i 2 mul\n"
+ " box\n"
+ " closepath\n"
+ " fill\n"
+ " i 1 sub /i exch def\n"
+ " }for\n"
+ "newpath\n"
+ "0 setgray\n"
+ "0.4 setlinewidth\n"
+ "x y width height box\n"
+ "closepath\n"
+ "stroke\n"
+ "end\n"
+ "} bind def\n");
run(iter);
System.out.print("\n%%Trailer\n%%EOF\n");
return 0;
} catch (Exception err) {
error(err);
return -1;
} finally {
CloserUtil.close(r);
CloserUtil.close(iter);
}
}