Package fork.lib.bio.anno.genomic.region

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

34
35
36
37
38
39
40
41
   
   
   
protected void writeToFile(File out)throws Exception {
    GenomicRegionsComparator comp= new GenomicRegionsComparator(peaks, anno);
    GenomicRegionsBuilder gbout= comp.getNonIntersection();
    new BedExporter(gbout).writeToFile(out);
}
View Full Code Here
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
    File anno= new File(dir+"/anno/hg19_ensGene_exon.bed");
   
    File od= new File(d+"/novel");
   
    int side= 5000;
    GenomicRegionsBuilder gbanno= new GenomicRegionsModifier(
            new BedReader(anno).getGenomicRegionsBuilder()).getExtendedRegions(side, side);
   
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File pf= fs[i];
        if(FileName.getExt(pf).equals("bed")){
            GenomicRegionsBuilder gbpeak= new BedReader(pf).getGenomicRegionsBuilder();
            GetNovelPeaks gn= new GetNovelPeaks(gbpeak, gbanno);

            File out= new File(od+"/novel_"+ pf.getName());
            gn.writeToFile(out);
        }
View Full Code Here
35
36
37
38
39
40
41
42
43
44
45
   
    File[] fs = d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed")){
            GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
            SplicedBedReader sr= new SplicedBedReader(anno);

            File od= new File(d+"/locate/"+ FileName.getBaseName(anno)+"/"+FileName.getBaseName(f));
            SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
            ll.writeToDir(od, "locate");
View Full Code Here
44
45
46
47
48
49
50
51
52
53
54
    //File anno= new File(dir+"/anno/refseq_hg19_exon.bed");
    File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
   
    File out= new File(d+"/locate_"+FileName.getBaseName(anno)+".bed");
   
    GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
    SplicedBedReader sr= new SplicedBedReader(anno);
   
    SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
    ll.writeToFile(out);
   
View Full Code Here
52
53
54
55
56
57
58
59
60
61
62
    File dir= Dirs.getFile("dir");
    File od= new File(dir+"/data/human_magnus/h2az/norm/peak/novel/scoreChip");
    File cd= new File(dir+"\\data\\human_magnus\\h2az\\norm");
    File rf= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak\\novel/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
View Full Code Here
55
56
57
58
59
60
61
62
63
64
65
    //File d= new File(dir+"/data\\human_magnus\\h2az\\norm\\peak/merge");
    File d= new File(dir+"/data\\human_magnus\\h2az/macs/merge");
    File od= new File(d+"/scoreNorm");
    File rf= new File(d+"/merge.bed");
   
    GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
   
    File[] fs= cd.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
View Full Code Here
29
30
31
32
33
34
35
36
37
38
39
40
   
public void addMergeFile(File f)throws Exception {
    String cntag= FileName.getBaseName(f);
    HashMap<String, String> hma= new HashMap<>();
    HashMap<String, String> hmb= new HashMap<>();
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String u= gr.chr+":"+(int)gr.low+"-"+(int)gr.high;
        hma.put( u, gr.getID());
        hmb.put( u, Double.toString(gr.getValue()));
View Full Code Here
33
34
35
36
37
38
39
40
41
42
43
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            mer.mergeNoSort(gb);
        }
        mer.sort();
        new BedExporter(mer.getMergedGenomicRegionsBuilder()).writeToFile(out);
    }
View Full Code Here
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
    double sthr= 0.6;
    double zthr= 80;
    File dir= Dirs.getFile("dir");
   
   
    GenomicRegionsBuilder gbl= new BedReader(new File(dir+"/anno/bed/len/len_150_off_0.bed")).getGenomicRegionsBuilder();
    ArrayList<LandscapeScoringResultEntry> rsz= new LandscapeScoring(
            new BedGraphReader(new File(dir+"/data/chip-seq/norm/norm_wig_chip_742-wt_r1_sacCer1.wig")).getLandscapeBuilder(),
            gbl
            ).getResultEntries();
   
    LandscapeBuilder lbs= new BedGraphReader(new File(dir+"/other_datasets/venters_2009/Swr1_MAT01.bar.wig")).getLandscapeBuilder();
    ArrayList<LandscapeScoringResultEntry> rss= new LandscapeScoring(
            lbs, gbl
            ){
            protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                double max= 0;
                for(int i=0; i<bufs.size() ; i++){
                    double v= (Double) bufs.get(i).attribute();
                    if(v>max){
                        max=v;
                    }
                }
                return new double[]{max};
            }
            }.getResultEntries();
   
   
   
    HashMap<GenomicRegion, Double> maps= LandscapeScoringResultEntry.toHashMap(rss, 0);
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    for(int i=0; i<rsz.size() ; i++){
        LandscapeScoringResultEntry rz= rsz.get(i);
        double vz= rz.scores[0], vs= maps.get(rz.gr);
       
        if(vz>zthr && vs<sthr){
            System.out.println(rz.gr.toUCSCFormat()+"  "+ vz+"  "+ vs);
            gbout.add(rz.gr);
        }
    }
    gbout.join(0);
    gbout.writeToFileBed(new File("out/swr1_z.bed"));
   
}
View Full Code Here
31
32
33
34
35
36
37
38
39
40
41
    File ld= new File(d+"/lineup");
    //File regf= new File(ld+"/chr3_cn3300_cz3.bed");
    File regf= new File(ld+"/chr3_cn3300_cnz3.bed");
   
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
    GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
    gb= gm.getThreePrimeEnds(300, 100);
   
    File od= new File(ld+"/"+FileName.getBaseName(regf));
    ArrayList<File> fs= new ArrayList<>();
View Full Code Here
TOP

Related Classes of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder

  • data.cerevisiae.at.ATContentBp
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper$ProbeMapperStrand
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
  • data.cerevisiae.inhouse.a_score.ScoreRNAGeneRead
  • data.cerevisiae.inhouse.chip.ChipChipRemoveExtreme
  • data.cerevisiae.inhouse.spikein.ScoreSpike
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.