Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.BedReader

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    File dir = Dirs.getFile("dir");
   
    File d= new File(dir+"/anno\\bed\\sacCer1-xu\\orient");
    File f= new File(d+"/orient3.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
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    GetSequenceFasta get= new GetSequenceFasta(new File(dir+"/anno/genomes/sacCer1/sacCer1.fa"));
   
    for( int i=0; i<10; i++ ){
        File f= new File(d+"/bin_"+i+".bed");
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        ToSeq tt= new ToSeq(gb, get);
        File of= new File(od+"/seq_"+FileName.getBaseName(f)+".fasta");
        tt.writeToFile(of);
    }
   
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        "749-htz1oe_ypg_20140313-r2_pe1",
    };
   
    File outd= new File(datd+"/score/");
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    for( int i=0; i<samps.length ; i++ ){
    //for( int i=0; i<1 ; i++ ){
        String samp= samps[i];
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        "0"
    };
    for( int i=0; i<ts.length; i++ ){
        String t= ts[i];
        File rf= new File(d+"/peak_norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.bed");
        GenomicRegionsBuilder gb= new BedReader(rf).getGenomicRegionsBuilder();
       
        File f= new File(cd+"/norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.wig");
        LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
        File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
        ScoreChipNormEach ss= new ScoreChipNormEach(gb, lb);
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protected void init() throws Exception{
    hm= new HashSet();
    hmnot= new HashSet();
    GenomicRegionsBuilder gb= new BedReader(file).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbc= new BedReader(chr).getGenomicRegionsBuilder();
    HashMap<String, GenomicRegion> cr= new HashMap<>();
    Iterator<GenomicRegion> it= gbc.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        cr.put(gr.chr, gr);
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    //for( int i=0; i<1 ; i++ ){
        String t= ts[i];
        String tt= tag+"_"+t;
        File f= new File(d+"/select_"+tt+".bed");
        GenomicRegionsLocator gl= new GenomicRegionsLocator(
                new BedReader(f).getGenomicRegionsBuilder(),
                new BedReader(rf).getGenomicRegionsBuilder()
            );
        File out= new File(od+"/location_"+tt+".bed");
        gl.writeToFile(out);
    }
   
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public static void main(String[] args) throws Exception {
    File dir= Dirs.getFile("dir");
    File fd= new File(dir+"/data/rna");
    File f= new File("out/score/set/sacCer1-xu/scan/intra_300_0_10_51.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    String s= "884-rrp6d-wt";
    LandscapeBuffer lbf= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_for.wig"));
    LandscapeBuffer lbr= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_rev.wig"));
    System.out.println(1);
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    File compf= new File(dir+"/other_datasets\\statham2014_mcf7-mods\\norm\\peaks\\locate\\ensGene_hg19_exon/locate_peak_norm_wig_mcf7_h3k4me1_SRR1282220_hg19.bed");
    //File compf= new File(dir+"/other_datasets\\statham2014_mcf7-mods\\norm\\peaks\\locate\\ensGene_hg19_exon/locate_peak_norm_wig_mcf7_h3k27ac_SRR1282218_hg19.bed");
    //File compf= new File(dir+"/other_datasets/statham2014_mcf7-mods/GSM1383850_MCF7_NDR_locate.bed");
   
    GenomicRegionsBuilder gbcomp= new BedReader(compf).getGenomicRegionsBuilder();
   
    String[] ts= new String[]{
        "0"
    };
    for( int i=0; i<ts.length; i++ ){
        String t= ts[i];
        File f= new File(d+"/peak_norm_wig_mcf7_chip-h2az_time-"+t+"_hg19.bed");
       
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
        String tag= FileName.getBaseName(compf);
        LinkChip ll= new LinkChip(gb, gbcomp);
        File out= new File(od+"/"+tag+"/time-"+t+"_"+tag+".bed");
        ll.writeToFile(out);
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protected File f;
protected LandscapeBuilder lbf, lbr;
   
   
    public Fuck2(File f, LandscapeBuilder lbf, LandscapeBuilder lbr)throws Exception {
        GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
       
        String[] chrs= gb.getUnsortedChromosomeList();
        for( int i=0; i<chrs.length ; i++ ){
            String chr= chrs[i];
            if(lbf.containsChromosome(chr) && lbr.containsChromosome(chr) ){
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    //File lbf= new File("/home/forksapien/mystudy/phd/files/data/chip-seq/norm/norm_744.wig");
   
   
    LandscapeScoring ls= new LandscapeScoring(
            new BedGraphReader(lbf).getLandscapeBuilder(),
            new BedReader(reg).getGenomicRegionsBuilder()
            );
   
    File out = new File(d+"/score/score_"+ FileName.getBaseName(lbf)+"_"+FileName.getBaseName(reg)+".bed");
    ls.writeToBedFile(out);
   
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Related Classes of fork.lib.bio.anno.genomic.BedReader

  • 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.ScoreChipGene
  • data.cerevisiae.inhouse.a_score.ScoreChipSeqGene
  • data.cerevisiae.inhouse.a_score.ScoreLen
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.cerevisiae.inhouse.a_score.ScoreRNAAnti
  • data.cerevisiae.inhouse.a_score.ScoreRNAGene
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