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@jernst98
jernst98 committed Jul 5, 2020
1 parent 9987049 commit cdfca66
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Showing 7 changed files with 454 additions and 57 deletions.
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311 changes: 307 additions & 4 deletions edu/mit/compbio/ChromHMM/BrowserOutput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -385,7 +385,7 @@ public void makebrowserdense() throws IOException
String szID = szFullID.substring(1); //this removes ordering type
if (bfirst)
{
String szout = "track name=\""+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
String szout = "track name=\""+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
+" ordered)"+"\" visibility=1 itemRgb=\"On\""+"\n";
byte[] btformat = szout.getBytes();
pwzip.write(btformat,0,btformat.length);
Expand Down Expand Up @@ -433,7 +433,7 @@ public void makebrowserdense() throws IOException
String szID = szFullID.substring(1); //this removes ordering type
if (bfirst)
{
pw.println("track name=\""+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
pw.println("track name=\""+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szFullID.charAt(0))
+" ordered)"+"\" visibility=1 itemRgb=\"On\"");
bfirst = false;
}
Expand Down Expand Up @@ -559,7 +559,7 @@ public void makebrowserexpanded() throws IOException
if (bgzip)
{
GZIPOutputStream pwzip = new GZIPOutputStream(new FileOutputStream(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed.gz"));
String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\""+"\n";
byte[] btformat = szout.getBytes();
pwzip.write(btformat,0,btformat.length);
Expand Down Expand Up @@ -641,7 +641,7 @@ public void makebrowserexpanded() throws IOException
else
{
PrintWriter pw = new PrintWriter(new FileWriter(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed"));
pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\"");
int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);
Expand Down Expand Up @@ -699,5 +699,308 @@ public void makebrowserexpanded() throws IOException
pw.close();
}
}




//////////////////////////////////////////////////////////////////////////////////////////////////
/**
* Makes a single track browser view of the segmentation represented in szsegmentfile
* szcolormapping is a two or three column text file which maps state ID to R,G,B color triples and optionally a state label
* Name of segmentation in the browser file is given by szsegmentationame
* Output is a file named szoutputfileprefix_browserdense.bed of segmentation viewable with one state per row
*/
public void makebrowserexpandedLowMem() throws IOException
{
if (bgzip)
{
System.out.println("Writing to file "+szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed.gz");
}
else
{
System.out.println("Writing to file "+szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed");
}

String szLine;

BufferedReader brsegment = Util.getBufferedReader(szsegmentfile);

//stores set of chromosomes and labels
HashSet hschroms = new HashSet();
HashSet hslabels = new HashSet();

//stores for each chromosome the maximum coordinate
HashMap hmchromMax = new HashMap();


//maps a label without the prefix back to the full label
HashMap hmlabelToFull = new HashMap();

String szLabelFull=null;
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
String szLabel = szLabelFull.substring(1);

hmlabelToFull.put(szLabel, szLabelFull);

hschroms.add(szchrom);
hslabels.add(szLabel);
//ArrayList alRecs = (ArrayList) hmcoords.get(szchrom+"\t"+szLabel);
//if (alRecs ==null)
//{
//creating first entry for chromsome and coordinate
// alRecs = new ArrayList();
// hmcoords.put(szchrom+"\t"+szLabel,alRecs);
//}
//alRecs.add(new BeginEndRec(nbegin,nend));

//potentially updating maximum coordinate for chromosome
Object obj = ((Integer) hmchromMax.get(szchrom));
if (obj != null)
{
int nval = ((Integer) obj).intValue();

if (nend > nval)
{
hmchromMax.put(szchrom,Integer.valueOf(nend));
}
}
else
{
hmchromMax.put(szchrom,Integer.valueOf(nend));
}
}
brsegment.close();


//gets all the state labels and sorts them
String[] szLabels = new String[hslabels.size()];
Iterator itrLabels = hslabels.iterator();
int nindex = 0;
while (itrLabels.hasNext())
{
szLabels[nindex] = (String) itrLabels.next();
nindex++;
}
Arrays.sort(szLabels, new LabelCompare());

//gets all the chromsomes and sorts them
String[] szChroms = new String[hschroms.size()];
Iterator itrChroms = hschroms.iterator();
nindex = 0;
while (itrChroms.hasNext())
{
szChroms[nindex] = (String) itrChroms.next();
nindex++;
}
Arrays.sort(szChroms);

if (bgzip)
{
GZIPOutputStream pwzip = new GZIPOutputStream(new FileOutputStream(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed.gz"));
String szout = "track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\""+"\n";
byte[] btformat = szout.getBytes();
pwzip.write(btformat,0,btformat.length);

//pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
// +" ordered)"+"\" visibility=2 itemRgb=\"On\"");
int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;

szout = "browser position "+szChroms[0]+":1-"+nbrowserend+"\n";
btformat = szout.getBytes();
pwzip.write(btformat,0,btformat.length);
//pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);

for (int nchrom = 0; nchrom < szChroms.length; nchrom++)
{
HashMap hmcoords = new HashMap();
String szcurrchrom = szChroms[nchrom];

//stores the set of interval coordinates for each chromosome and label
brsegment = Util.getBufferedReader(szsegmentfile);
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
if (szchrom.equals(szcurrchrom))
{
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
String szLabel = szLabelFull.substring(1);

ArrayList alRecs = (ArrayList) hmcoords.get(szLabel);
if (alRecs ==null)
{
//creating first entry for chromsome and coordinate
alRecs = new ArrayList();
hmcoords.put(szLabel,alRecs);
}
alRecs.add(new BeginEndRec(nbegin,nend));
}
}
brsegment.close();


//UCSC browser seems to reverse the ordering of browser track files
for (int nlabel = szLabels.length-1; nlabel >=0; nlabel--)
{
String szcolor = (String) hmcolor.get(""+szLabels[nlabel]);
//omits those segment labels not observed at all on chromosome

ArrayList alRecs = (ArrayList) hmcoords.get(szLabels[nlabel]);
if (alRecs == null) continue;

int nmax = ((Integer) hmchromMax.get(szChroms[nchrom])).intValue();

//this forces browser to display segment until the end of the chromosome
alRecs.add(new BeginEndRec(nmax-1,nmax));

int nsize = alRecs.size();
int nmin = ((BeginEndRec) alRecs.get(0)).nbegin;
int nfinalend = nmax;

String szoutlabel;
String szsuffix;
if ((szsuffix = (String) hmlabelExtend.get((String) hmlabelToFull.get(szLabels[nlabel])))!=null)
{
szoutlabel = szLabels[nlabel]+"_"+szsuffix;
}
else
{
szoutlabel = szLabels[nlabel];
}

StringBuffer sbout = new StringBuffer();
sbout.append(szcurrchrom+"\t"+0+"\t"+nfinalend+"\t"+szoutlabel+"\t0\t.\t"+nmin+"\t"+nfinalend+"\t"+szcolor+"\t"+(nsize+1)+"\t");
//pw.print(szChroms[nchrom]+"\t"+0+"\t"+nfinalend+"\t"+szoutlabel+"\t0\t.\t"+nmin+"\t"+nfinalend+"\t"+szcolor+"\t"+(nsize+1)+"\t");
//pw.print(0); //forcing the display to start at the beginning of the chromosome
sbout.append(0);
for (int ni = 0; ni < nsize; ni++)
{
BeginEndRec theBeginEndRec = (BeginEndRec) alRecs.get(ni);
int ndiff = theBeginEndRec.nend - theBeginEndRec.nbegin;
sbout.append(",");
sbout.append(ndiff);
//pw.print(",");
//pw.print(ndiff);
}
sbout.append("\t");
sbout.append(0);
//pw.print("\t");
//pw.print(0);
for (int ni = 0; ni < nsize; ni++)
{
int nloc = ((BeginEndRec) alRecs.get(ni)).nbegin;
sbout.append(",");
sbout.append(nloc);
//pw.print(",");
//pw.print(nloc);
}
sbout.append("\n");
// pw.println();
btformat = sbout.toString().getBytes();
pwzip.write(btformat,0,btformat.length);
}
}
pwzip.finish();
pwzip.close();
}
else
{
PrintWriter pw = new PrintWriter(new FileWriter(szoutputfileprefix+ChromHMM.SZBROWSEREXPANDEDEXTENSION+".bed"));
pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\""+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))
+" ordered)"+"\" visibility=2 itemRgb=\"On\"");
int nbrowserend = (int) (((Integer)hmchromMax.get(szChroms[0])).intValue()*.001)+1;
pw.println("browser position "+szChroms[0]+":1-"+nbrowserend);

for (int nchrom = 0; nchrom < szChroms.length; nchrom++)
{
String szcurrchrom = szChroms[nchrom];
HashMap hmcoords = new HashMap();

//stores the set of interval coordinates for each chromosome and label
brsegment = Util.getBufferedReader(szsegmentfile);
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
if (szchrom.equals(szcurrchrom))
{
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
String szLabel = szLabelFull.substring(1);

ArrayList alRecs = (ArrayList) hmcoords.get(szLabel);
if (alRecs ==null)
{
//creating first entry for chromsome and coordinate
alRecs = new ArrayList();
hmcoords.put(szLabel,alRecs);
}
alRecs.add(new BeginEndRec(nbegin,nend));
}
}
brsegment.close();

//UCSC browser seems to reverse the ordering of browser track files
for (int nlabel = szLabels.length-1; nlabel >=0; nlabel--)
{
String szcolor = (String) hmcolor.get(""+szLabels[nlabel]);

//omits those segment labels not observed at all on chromosome
ArrayList alRecs = (ArrayList) hmcoords.get(szLabels[nlabel]);
if (alRecs == null) continue;

int nmax = ((Integer) hmchromMax.get(szChroms[nchrom])).intValue();

//this forces browser to display segment until the end of the chromosome
alRecs.add(new BeginEndRec(nmax-1,nmax));

int nsize = alRecs.size();
int nmin = ((BeginEndRec) alRecs.get(0)).nbegin;
int nfinalend = nmax;

String szoutlabel;
String szsuffix;
if ((szsuffix = (String) hmlabelExtend.get((String) hmlabelToFull.get(szLabels[nlabel])))!=null)
{
szoutlabel = szLabels[nlabel]+"_"+szsuffix;
}
else
{
szoutlabel = szLabels[nlabel];
}

pw.print(szcurrchrom+"\t"+0+"\t"+nfinalend+"\t"+szoutlabel+"\t0\t.\t"+nmin+"\t"+nfinalend+"\t"+szcolor+"\t"+(nsize+1)+"\t");
pw.print(0); //forcing the display to start at the beginning of the chromosome
for (int ni = 0; ni < nsize; ni++)
{
BeginEndRec theBeginEndRec = (BeginEndRec) alRecs.get(ni);
int ndiff = theBeginEndRec.nend - theBeginEndRec.nbegin;
pw.print(",");
pw.print(ndiff);
}
pw.print("\t");
pw.print(0);
for (int ni = 0; ni < nsize; ni++)
{
int nloc = ((BeginEndRec) alRecs.get(ni)).nbegin;
pw.print(",");
pw.print(nloc);
}
pw.println();
}
}
pw.close();
}
}
}

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