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

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

74
75
76
77
78
79
80
81
82
83
84
        "htz1",
        "k8ac",
        "k10ac",
        "k14ac"
    };
    GenomicRegionsBuilder gb= new BedReader(new File(dir+"/anno/sacCer1_chr.bed")).getGenomicRegionsBuilder();
   
    for(int i=0; i<fs.length ; i++){
        String ty= fs[i];
        File f= new File(d+"/norm_"+ty+".wig");
        ChipChipRemoveExtreme cc= new ChipChipRemoveExtreme(
View Full Code Here
68
69
70
71
72
73
74
75
76
77
    File od= new File(dir+"/anno/bed/"+org);
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    GenerateGenic gg= new GenerateGenic(gb);
    gg.writeToDirectory(od, org);
}
View Full Code Here
38
39
40
41
42
43
44
45
46
47
48
    File dir= Dirs.getFile("dir");
    File d= new File(dir+"/test_anal/lambda");
    File anno= new File(d+"/lambda.bed");
    File od= new File(d+"/score/lambda");
   
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
   
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("wig")){
View Full Code Here
86
87
88
89
90
91
92
93
94
95
96
        for( int j=0; j<regfs.length ; j++ ){
            File f= new File(regd+"/"+ty+regfs[j]);
            String tag= FileName.getBaseName(f);
            File od= new File(outd+"/"+samp+"_antisense");

            GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
            ScoreRNAAnti sc= new ScoreRNAAnti(gb, lbr, lbf);
            sc.writeToFile( new File(od+"/"+samp+"_antisense_"+tag+".bed") );
        }
    }
   
View Full Code Here
34
35
36
37
38
39
40
41
42
    }

public void writeToFile(File out)throws Exception {
    File dir= Dirs.getFile("dir");
    File anno= new File(dir+"/anno/bed/sacCer1-xu/sacCer1-xu_gene_five_0.150.bed");
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
    LandscapeScoring ls= new LandscapeScoring(lb ,gb);
    ls.writeToBedFile(out);
}
View Full Code Here
60
61
62
63
64
65
66
67
68
69
70
    File d= new File(dir+"/anno/bed/sacCer1");
    File anno = new File(dir+"/anno/sacCer1_chr.bed");
   
    int len= 10;
   
    GenomicRegionsBuilder gb= new BedReader(anno).getGenomicRegionsBuilder();
   
    GenerateWindowsNonOverlapping gg= new GenerateWindowsNonOverlapping(gb, len);
    gg.writeToFile(new File(d+"/window/non-ol_"+ len+"_"+FileName.getBaseName(anno)+".bed"));
   
}
View Full Code Here
82
83
84
85
86
87
88
89
90
91
92
            tags.add(t);
        }
    }
   
    File outd= new File(datd+"/score/"+ty);
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    Iterator<String> it= tags.iterator();
    while(it.hasNext()){
        String samp= it.next();
View Full Code Here
50
51
52
53
54
55
56
57
58
59
60
public void writeToDir(File od)throws Exception {
    od.mkdirs();
    ArrayList<Double> bs= dis.quantileBoundaries(binn);
    ArrayList<GenomicRegionsBuilder> gbouts= new ArrayList<>();
    for( int i=0; i<binn; i++ ){
        gbouts.add(new GenomicRegionsBuilder());
    }
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        double v= gr.getValue() ;
View Full Code Here
78
79
80
81
82
83
84
85
86
87
88
public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File d = new File(dir+"/other_datasets/lee_2007_nucleosome/pref");
    File f= new File(d+"/score_non-ol_10_sacCer1_chr.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    int binn = 10;
   
    Bin  bb= new Bin(gb, binn);
    bb.writeToDir(d);
View Full Code Here
127
128
129
130
131
132
133
134
135
136
137
        "1054-wt-gdna_sd-ura_20140313-r2_pe1"
    };
   
    File od= new File(datd+"/norm");
   
    GenomicRegionsBuilder gb= new BedReader(regf).getGenomicRegionsBuilder();
   
       
    for( int i=0; i<samps.length ; i++ ){
        String samp= samps[i];
       
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.