Package fork.lib.bio.seq

Examples of fork.lib.bio.seq.FastaReader

89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
   
    while( (en=zz.nextEntry())!=null ){
        String nm= en.tit;
        PWM mot= en.pwm;
       
        FastaReader fr= new FastaReader(new File(dir+"/anno/genomes/sacCer1/sacCer1.fa"));
        MotifToLandscape ml= new MotifToLandscape(fr, mot);
       
        System.out.println(nm+"  ");
        File of= new File(od+"/"+nm+".wig");
        ml.writeToFile(of, nm);
        fr.close();
       
           
        /*
        String s= "AGATTATTTAATAATGGGAC";
        double a= mot.align(s);
View Full Code Here
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
   
    int size= 1;
   
   
    FrequencyCount<String> fcg= new FrequencyCount();
    FastaReader frg= new FastaReader(genomef);
    FastaEntry eng;
    while( (eng=frg.nextEntry())!=null ){
        String s= eng.getSequence();
        for( int i=0; i<s.length()-size; i++ ){
            String ss= s.substring(i, i+size);
            fcg.add(ss);
        }
    }
    Object[] ks= fcg.getSortedKeys();
   
   
    File[] fs= d.listFiles();
    for( int j=0; j<fs.length; j++ ){
        File f= fs[j];
        if(FileName.getExt(f).equals("fasta")){
            FastaReader fr= new FastaReader(f);
            FastaEntry en;
            FrequencyCount<String> fc= new FrequencyCount<>();


            while( (en=fr.nextEntry())!=null ){
                String s= en.getSequence();
                for( int i=0; i<s.length()-size; i++ ){
                    String ss= s.substring(i, i+size);
                    fc.add(ss);
                }
View Full Code Here
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
                    tab.appendEmptyColumn(col);
                }
                tab.setValueAt(v, row, col);
            }
        }
        FastaReader fr= new FastaReader(new File(dir+"/anno/genomes/sacCer1/sacCer1.fa"));
        PWM mot= new PWM(tab);
        MotifToLandscape ml= new MotifToLandscape(fr, mot);

        System.out.println(nm+"  ");
       
        File of= new File(od+"/"+nm+".wig");
        ml.writeToFile(of, nm);
        fr.close();
       
        //System.exit(1);
    }
   
   
View Full Code Here
26
27
28
29
30
31
32
33
34
35
36
37
38
39
   
public static void main(String[] args) throws Exception {
    File dir= Dirs.getFile("dir");
   
    File gen= new File(dir+"/anno/genomes/sacCer1/sacCer1.fa");
    FastaReader fr= new FastaReader(gen);
    BufferedWriter bw= new BufferedWriter(new FileWriter(new File(dir+"/anno/sacCer1_chr.bed")));
    FastaEntry en;
    while( (en=fr.nextEntry())!=null ){
        String chr= en.getTitle();
        int l= en.getSequence().length();
        bw.write(chr+"\t0\t"+l+"\t"+chr+"\t0\t+\n");
    }
    bw.close();
View Full Code Here
TOP

Related Classes of fork.lib.bio.seq.FastaReader

  • data.cerevisiae.region.GenerateChr
  • data.cerevisiae.test.regseq.FindMotif
  • data.cerevisiae.tfpwm.BadisToLandscape
  • data.cerevisiae.tfpwm.ZhuToLandscape
    • 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.