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Version 1.19
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Added '-labels' option to OverlapEnrichment and NeighborhoodEnrichment

Added '-reordercolsmodelfile' to Reorder

Added error checking that headers of binarized data are in same order as in the model file.
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@jernst98
jernst98 committed Jun 25, 2019
1 parent af25686 commit 42f5c0c
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Showing 5 changed files with 1,019 additions and 537 deletions.
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92 changes: 64 additions & 28 deletions edu/mit/compbio/ChromHMM/ChromHMM.java
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Original file line number Diff line number Diff line change
Expand Up @@ -547,12 +547,16 @@ public class ChromHMM
String szreorderoutbedfile;



/**
* Indicate the beta's should be rescaled separately and also enforces that no beta value goes below STATEEPSILON or alpha if emission is greater than 0
*/
boolean bscalebeta;

/**
* True if should also reorder the columns of the model file
*/
boolean breordercolsmodel;

///////////////////////////////////////////////////////////////////////////////////////////////////////////////
/**
* Stores an integer index and array of boolean flags
Expand Down Expand Up @@ -825,7 +829,8 @@ private void makeLabelMapping(String szlabelmapping) throws IOException
*/
public ChromHMM(String szInitFile, String szoutputdir, String szstateorderingfile, String szcolumnorderingfile,
String szoutfileID,int nstateorder,boolean bordercols,Color theColor,
String szlabelmapping, boolean bprintimage,String szreorderinbedfile, String szreorderoutbedfile) throws IOException
String szlabelmapping, boolean bprintimage,String szreorderinbedfile, String szreorderoutbedfile,
boolean breordercolsmodel) throws IOException
{
this.szcolumnorderingfile = szcolumnorderingfile;
this.szInitFile = szInitFile;
Expand All @@ -839,7 +844,7 @@ public ChromHMM(String szInitFile, String szoutputdir, String szstateorderingfil

this.szreorderinbedfile = szreorderinbedfile;
this.szreorderoutbedfile = szreorderoutbedfile;

this.breordercolsmodel = breordercolsmodel;
hmlabelExtend = new HashMap();
makeLabelMapping(szlabelmapping);

Expand Down Expand Up @@ -1728,11 +1733,23 @@ private void printParametersToFile(int niteration) throws IOException
double[][] emissionprobs_stateordering_ni = emissionprobs[stateordering[ni]];
for (int nj = 0; nj < emissionprobs_stateordering_ni.length; nj++)
{
double[] emissionprobs_stateordering_ni_nj = emissionprobs_stateordering_ni[nj];
for (int nk = 0; nk < emissionprobs_stateordering_ni_nj.length; nk++)
{
pw.println("emissionprobs\t"+(ni+1)+"\t"+nj+"\t"+datasets[nj]+"\t"+nk+"\t"+emissionprobs_stateordering_ni_nj[nk]);
}
double[] emissionprobs_stateordering_ni_nj;
String szdataset;
if (breordercolsmodel)
{
emissionprobs_stateordering_ni_nj = emissionprobs_stateordering_ni[colordering[nj]];
szdataset = datasets[colordering[nj]];
}
else
{
emissionprobs_stateordering_ni_nj = emissionprobs_stateordering_ni[nj];
szdataset = datasets[nj];
}

for (int nk = 0; nk < emissionprobs_stateordering_ni_nj.length; nk++)
{
pw.println("emissionprobs\t"+(ni+1)+"\t"+nj+"\t"+szdataset+"\t"+nk+"\t"+emissionprobs_stateordering_ni_nj[nk]);
}
}
}
pw.close();
Expand Down Expand Up @@ -2964,13 +2981,15 @@ else if (szvartype.equalsIgnoreCase("emissionprobs"))
{
int nstate = Integer.parseInt(st.nextToken())-1;
int nmod = Integer.parseInt(st.nextToken());
String szdataset = st.nextToken();
if (datasets[nmod]==null)
{
datasets[nmod] = st.nextToken();
datasets[nmod] = szdataset;//st.nextToken();
}
else
else if (!szdataset.equals(datasets[nmod]))
{
st.nextToken();
throw new IllegalArgumentException("For mark "+nmod+" in model file found "+szdataset+", but expecting "+datasets[nmod]+"."
+" This might be because columns of binarized file are in a different order from model learning.");
}
int nval = Integer.parseInt(st.nextToken());
double dprob = Double.parseDouble(st.nextToken());
Expand Down Expand Up @@ -3957,6 +3976,7 @@ else if (szincludemarks.charAt(nmark) == '0')
String szLine;
br.readLine(); //first line tells cell type and chromosome
br.readLine();//flush mark header

ArrayList aldata = new ArrayList();
while ((szLine = br.readLine())!=null)
{
Expand Down Expand Up @@ -11721,8 +11741,8 @@ public void loadDataFileStubs() throws IOException
int ntoken = 0;
while (st.hasMoreTokens())
{
datasets[ntoken] = st.nextToken();
ntoken++;
datasets[ntoken] = st.nextToken();
ntoken++;
}
//numdatasets is the number of marks we are integrating
numdatasets = datasets.length;
Expand Down Expand Up @@ -12067,8 +12087,8 @@ public void loadData() throws IOException
int ntoken = 0;
while (st.hasMoreTokens())
{
datasets[ntoken] = st.nextToken();
ntoken++;
datasets[ntoken] = st.nextToken();
ntoken++;
}
}
else
Expand Down Expand Up @@ -12257,7 +12277,7 @@ public static void main(String[] args) throws IOException

if (szcommand.equalsIgnoreCase("Version"))
{
System.out.println("This is Version 1.18 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
System.out.println("This is Version 1.19 of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology");
}
else if ((szcommand.equals("BinarizeBam"))||(szcommand.equalsIgnoreCase("BinarizeBed")))
{
Expand Down Expand Up @@ -13180,6 +13200,7 @@ else if (szcommand.equalsIgnoreCase("OverlapEnrichment"))
boolean bbaseres = ChromHMM.DEFAULT_OVERLAPENRICHMENT_BBASERES; //boolean ChromHMM.DEFAULT_OVERLAPENRICHMENT_BBASERES = true;
String szoutfile;
boolean buniformheat = ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT; //boolean ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT = false;
boolean bstringlabels = false;


String sztitle = "Fold Enrichments";
Expand Down Expand Up @@ -13249,6 +13270,10 @@ else if (args[nargindex].equals("-center"))
{
bcenter = true;
}
else if (args[nargindex].equals("-labels"))
{
bstringlabels = true;
}
else if (args[nargindex].equals("-m"))
{
szlabelmapping = args[++nargindex];
Expand Down Expand Up @@ -13304,12 +13329,12 @@ else if (args[nargindex].equals("-lowmem"))
if (blowmem)
{
StateAnalysis.enrichmentMaxLowMem(szinput, szinputcoorddir,szinputcoordlist,noffsetleft,noffsetright,nbinsize,
bcenter, bunique, busesignal,szcolfields,bbaseres, szoutfile,bcolscaleheat,theColor,sztitle, szlabelmapping, bprintimage);
bcenter, bunique, busesignal,szcolfields,bbaseres, szoutfile,bcolscaleheat,theColor,sztitle, szlabelmapping, bprintimage,bstringlabels);
}
else
{
StateAnalysis.enrichmentMax(szinput, szinputcoorddir,szinputcoordlist,noffsetleft,noffsetright,nbinsize,
bcenter, bunique, busesignal,szcolfields,bbaseres, szoutfile,bcolscaleheat,theColor,sztitle, szlabelmapping,bprintimage);
bcenter, bunique, busesignal,szcolfields,bbaseres, szoutfile,bcolscaleheat,theColor,sztitle, szlabelmapping,bprintimage,bstringlabels);
}
}
else
Expand All @@ -13326,7 +13351,7 @@ else if (args[nargindex].equals("-lowmem"))
if (!bok)
{
System.out.println("usage OverlapEnrichment [-a cell][-b binsize][-binres][-color r,g,b][-center][-colfields chromosome,start,end[,signal]]"+
"[-e offsetend][-f coordlistfile][-lowmem][-m labelmappingfile]"+
"[-e offsetend][-f coordlistfile][-labels][-lowmem][-m labelmappingfile]"+
"[-multicount][-noimage][-posterior][-s offsetstart][-signal][-t title][-uniformscale]"+
" inputsegment inputcoorddir outfileprefix");
}
Expand All @@ -13342,6 +13367,7 @@ else if ((szcommand.equalsIgnoreCase("NeighborhoodEnrichment"))||(szcommand.equa
String szlabelmapping = null;
boolean busestrand =ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESTRAND;
boolean busesignal = ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESIGNAL;
boolean bstringlabels = false;
String szcolfields = null;
int noffsetanchor = ChromHMM.DEFAULT_NEIGHBORHOOD_NOFFSETANCHOR;
String szoutfile;
Expand Down Expand Up @@ -13400,6 +13426,10 @@ else if (args[nargindex].equals("-l"))
{
numleft = Integer.parseInt(args[++nargindex]);
}
else if (args[nargindex].equals("-labels"))
{
bstringlabels = true;
}
else if (args[nargindex].equals("-lowmem"))
{
blowmem = true;
Expand Down Expand Up @@ -13474,12 +13504,12 @@ else if (bmax)
if (blowmem)
{
StateAnalysis.neighborhoodMaxLowMem(szinput,szanchorpositions,nbinsize,numleft,numright,
nspacing,busestrand,busesignal,szcolfields,noffsetanchor,szoutfile,theColor,sztitle,szlabelmapping, bprintimage);
nspacing,busestrand,busesignal,szcolfields,noffsetanchor,szoutfile,theColor,sztitle,szlabelmapping, bprintimage, bstringlabels);
}
else
{
StateAnalysis.neighborhoodMax(szinput,szanchorpositions,nbinsize,numleft,numright,
nspacing,busestrand,busesignal,szcolfields,noffsetanchor,szoutfile,theColor,sztitle,szlabelmapping, bprintimage);
nspacing,busestrand,busesignal,szcolfields,noffsetanchor,szoutfile,theColor,sztitle,szlabelmapping, bprintimage, bstringlabels);
}
}
else
Expand All @@ -13496,7 +13526,7 @@ else if (bmax)
if (!bok)
{
System.out.println("usage NeighborhoodEnrichment [-a cell][-b binsize][-color r,g,b][-colfields chromosome,position[,optionalcol1|,optionalcol1,optionalcol2]"+
"[-l numleftintervals][-lowmem][-m labelmappingfile][-noimage][-nostrand]"+
"[-l numleftintervals][-labels][-lowmem][-m labelmappingfile][-noimage][-nostrand]"+
"[-o anchoroffset][-posterior][-r numrightintervals]"+
"[-s spacing][-signal][-t title] inputsegment anchorpositions outfileprefix");
}
Expand Down Expand Up @@ -13998,7 +14028,7 @@ else if (args[nargindex].equals("-z"))
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BCENTER, !ChromHMM.DEFAULT_OVERLAPENRICHMENT_BCOUNTMULTI,
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUSESIGNAL,null,//szcolfields,
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BBASERES, szoutputdir+"/"+szprefix+ChromHMM.SZOVERLAPEXTENSION,
!ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT,theColor,"Fold Enrichment "+szprefix,null,bprintimage);
!ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT,theColor,"Fold Enrichment "+szprefix,null,bprintimage, false);
}
else
{
Expand All @@ -14010,7 +14040,7 @@ else if (args[nargindex].equals("-z"))
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BCENTER, !ChromHMM.DEFAULT_OVERLAPENRICHMENT_BCOUNTMULTI,
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUSESIGNAL,null,//szcolfields,
ChromHMM.DEFAULT_OVERLAPENRICHMENT_BBASERES, szoutputdir+"/"+szprefix+ChromHMM.SZOVERLAPEXTENSION,
!ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT,theColor,"Fold Enrichment "+szprefix,null,bprintimage);
!ChromHMM.DEFAULT_OVERLAPENRICHMENT_BUNIFORMHEAT,theColor,"Fold Enrichment "+szprefix,null,bprintimage, false);
}
String szoverlapoutfile = szprefix+ChromHMM.SZOVERLAPEXTENSION+".txt";
if (bprintimage)
Expand Down Expand Up @@ -14059,7 +14089,7 @@ else if (args[nargindex].equals("-z"))
ChromHMM.DEFAULT_NEIGHBORHOOD_NUMRIGHT, nbinsize,//nspacing
ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESTRAND,ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESIGNAL,null,//szcolfields,
ChromHMM.DEFAULT_NEIGHBORHOOD_NOFFSETANCHOR,szoutputdir+"/"+szprefix+"_"+szanchorname+"_neighborhood",
theColor,"Fold Enrichment "+szprefix+" "+szanchorname,null,bprintimage);
theColor,"Fold Enrichment "+szprefix+" "+szanchorname,null,bprintimage,false);
}
else
{
Expand All @@ -14068,7 +14098,7 @@ else if (args[nargindex].equals("-z"))
ChromHMM.DEFAULT_NEIGHBORHOOD_NUMRIGHT, nbinsize,//nspacing
ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESTRAND,ChromHMM.DEFAULT_NEIGHBORHOOD_BUSESIGNAL,null,//szcolfields,
ChromHMM.DEFAULT_NEIGHBORHOOD_NOFFSETANCHOR,szoutputdir+"/"+szprefix+"_"+szanchorname+"_neighborhood",
theColor,"Fold Enrichment "+szprefix+" "+szanchorname,null,bprintimage);
theColor,"Fold Enrichment "+szprefix+" "+szanchorname,null,bprintimage,false);
}
String szneighborhoodoutfileprefix = szprefix+"_"+szanchorname+ChromHMM.SZNEIGHBORHOODEXTENSION;

Expand Down Expand Up @@ -14128,6 +14158,7 @@ else if (szcommand.equalsIgnoreCase("Reorder"))
int nargindex = 1;
String szreorderinbedfile = null;
String szreorderoutbedfile = null;
boolean breordercolsmodel = false;

int nr=ChromHMM.DEFAULTCOLOR_R;
int ng=ChromHMM.DEFAULTCOLOR_G;
Expand Down Expand Up @@ -14168,6 +14199,10 @@ else if (args[nargindex].equals("-noimage"))
{
bprintimage = false;
}
else if (args[nargindex].equals("-reordercolsmodelfile"))
{
breordercolsmodel = true;
}
else if (args[nargindex].equals("-o"))
{
szstateorderingfile = args[++nargindex];
Expand Down Expand Up @@ -14249,7 +14284,8 @@ else if (args[nargindex].equals("-holdcolumnorder"))
boolean bprintsegments = !bnoprintsegment;
boolean bordercols = !bnoordercols;
ChromHMM theHMM = new ChromHMM(szInitFile, szoutputdir, szstateorderingfile, szcolumnorderingfile, szoutfileID,nstateorder,
bordercols,theColor,szlabelmapping,bprintimage, szreorderinbedfile, szreorderoutbedfile);
bordercols,theColor,szlabelmapping,bprintimage, szreorderinbedfile,
szreorderoutbedfile, breordercolsmodel);
theHMM.reorderModel();
}
}
Expand All @@ -14262,7 +14298,7 @@ else if (args[nargindex].equals("-holdcolumnorder"))
{

System.out.println("usage: Reorder [-color r,g,b][-f columnorderingfile][-holdcolumnorder][-i outfileID]"+
"[-m labelmappingfile][-noimage][-o stateorderingfile [-r bedfilein bedfileout]][-stateordering emission|transition] inputmodel outputdir");
"[-m labelmappingfile][-noimage][-o stateorderingfile [-r bedfilein bedfileout]][-reordercolsmodelfile][-stateordering emission|transition] inputmodel outputdir");

}
}
Expand Down
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