Package fork.lib.bio.seq.align

Examples of fork.lib.bio.seq.align.PWM

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                tab.appendEmptyColumn(col);
            }
            tab.setValueAt(v, row, col);
        }
    }
    PWM mot=new PWM(tab);
    return new PWMEntry(tit, mot);
}
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    PWMEntry en;
   
   
    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+"  ");
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    ZhuToLandscape zz= new ZhuToLandscape(tf);
    PWMEntry en;
    int ind=0;
    while((en=zz.nextEntry())!=null){
        String tit= en.tit;
        PWM mot= en.pwm;
        System.out.println("add: "+ tit);
       
        zg.addTF(tit, mot);
        ind++;
        //if(ind>5){break;}
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                }
                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");
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Related Classes of fork.lib.bio.seq.align.PWM

  • data.cerevisiae.tfpwm.BadisToLandscape
  • data.cerevisiae.tfpwm.ZhuToGene
  • data.cerevisiae.tfpwm.ZhuToLandscape
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