Previous Up Next

4  Usage of Lexique and Parti_simp



We give several examples of Lexique, to show how use its specific syntax. These examples are used on the DNA sequence of l-phage, in file lambda.seq, which is known to show strong signals of segmentation [Chu92, Chu89, Gué00].

In connection with Lexique, we give examples of computation and manipulation of partitionnings.
  1. We load the sequence.
    import sequence
    s=sequence.Sequence(fic="lambda.seq")
    
  2. We want to part this sequence such that a segment is described by a letter, and its value is the number of occurences of this letter.
    print s.alpha()
    import lexique
    lx1=lexique.Lexique()
    lx1.read_str('0:a 1:c 2:g 3:t')
    print lx1
    import parti_simp
    ps1=parti_simp.Parti_simp()
    ps1.mpp(s,lx1,100)
    
  3. We draw the even-numbered partitions.
    ps1.filter(lambda x: len(x)%2==0).draw_nf("lambda1.ps")
    
  4. We cluster the segments described by c or g, and the ones described by a or t, and sort the new Parti_simp following the number of segments. We draw the 20 first partitions of this new Parti_simp.
    ps2=ps1.group([[1,2],[0,3]])
    ps2.sort()
    ps2[:20].draw_nf("lambda1_cg.ps",seg=[1,2])
    


  5. We want to partition on comparing the occurences in c and g versus the ones in a and t.
    lx2=lexique.Lexique(str="0:+(cg) 1:+(at)")
    ps2=parti_simp.Parti_simp()
    ps2.mpp(s,lx2,20)
    ps2[:20].draw_nf("lambda2_cg.ps",num=1)
    



Previous Up Next