Package fork.lib.bio.anno.genomic

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

82
83
84
85
86
87
88
89
90
91
92
public static void main(String[] args) throws Exception {
    File dir= Dirs.getFile("dir");
    int len= 150;
   
    ATContentBp gg= new ATContentBp(
            new BedReader(new File(dir+"/anno/sacCer1_chr.bed")).getGenomicRegionsBuilder(),
            len,
            new File(dir+"/genomes/sacCer1/sacCer1.fa") );
   
    gg.writeToFile(new File(dir+"/anno/AT-content_"+len+"_sacCer1.wig"), "AT_content_"+len);
   
View Full Code Here
24
25
26
27
28
29
30
31
32
33
34
    File dir= Dirs.getFile("dir");
   
    File f= new File(dir+"/anno/raw/refGene_hg19_raw.bed");
    File of= new File(dir+"/anno/refGene_hg19.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    gb.removeRedundant();
    gb.sortAll();

   
    new BedExporter(gb).writeToFile(of);
View Full Code Here
40
41
42
43
44
45
46
47
48
49
50
        init();
    }
   
   
protected void init() throws Exception{
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    FastaSequenceExtractor se= new FastaSequenceExtractor(sf, gb);
    SequenceExtractorEntry en;
    while((en=se.nextEntry())!=null){
        GenomicRegion reg= en.getGenomicRegion();
        String seq= en.getSequence();
View Full Code Here
82
83
84
85
86
87
88
89
90
91
92
        "1054-wt-gdna_sd-ura_20140313-r2_pe1"
    };
   
    File outd= new File(datd+"/score/"+ty);
   
    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];
View Full Code Here
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
65
66
67
68
69
70
71
72
73
74
75
            File datf= new File(datd+"/norm_wig_chip_"+samp+"_"+rep+"_sacCer1.wig");
            //File datf= new File(datd+"/norm_"+samp+".wig");

            LandscapeScoring ls= new LandscapeScoring(
                new BedGraphReader(datf).getLandscapeBuilder(),
                new BedReader(reg).getGenomicRegionsBuilder()
                );

            File out = new File(outd+"/"+tag+"/set/score-len_"+ FileName.getBaseName(datf)+"_"+FileName.getBaseName(reg)+".bed");
            System.out.println(out);
            ls.writeToBedFile(out);
View Full Code Here
TOP

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
    • 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.