TFBS::Matrix Alignment
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
TFBS::Matrix::Alignment - class for alignment of PFM objects
Package variables
No package variables defined.
Included modules
Bio::Root::Root
File::Temp qw /:POSIX/
TFBS::Matrix
Inherit
Bio::Root::Root TFBS::Matrix
Synopsis
 * Making an alignment:
 
my $db_obj = TFBS::DB::JASPAR2->new
(-connect => ["dbi:mysql:JASPAR2:myhost",
"myusername", "mypassword"]);
my $pfm1 = $db_obj->get_Matrix_by_ID("M0001", "PFM");
my $pfm2 = $db_obj->get_Matrix_by_ID("M0002", "PFM");

my $alignment= new TFBS::Matrix::Alignment(
-pfm1=>$pfm1,
-pfm2=>$pfm2,
-binary=>"/TFBS/Ext/matrix_aligner",
);

Description
TFBS::Matrix::Alignment is a class for representing and performing
pairwise alignments of profiles (in the form of TFBS::PFM objects)
Alignments are preformed using a semi-global variant of the
Needleman-Wunsch algorithm that only permits the opening of one internal gap.
Fore reference, the algorithm is described in Sandelin et al
Funct Integr Genomics. 2003 Jun 25
Methods
alignmentDescriptionCode
gaps
No description
Code
lengthDescriptionCode
newDescriptionCode
scoreDescriptionCode
strandDescriptionCode
Methods description
alignmentcode    nextTop
 Title   : alignment
 Usage   : my $alignment_string = $alignmentobject->alignment();
 Function: access a string describing the alignment
 Returns : an string, where each number refers to a position in repective PFM.
 Position numbering is according to orientation: ie if the second profile is
 reversed, position 1 corresponds to the last position in the input profile.
 Gaps are denoted as - .

 RXR-VDR           -       1       2       3       -     4      5     -
 PPARgamma-RXRal   1       2       3       4       5     6      7     8

 Args    : none
lengthcodeprevnextTop
 Title   : length
 Usage   : my $length = $alignmentobject->length();
 Function: access the length of an alignment (ie thenumber of aligned positions)
 Returns : an integer
 Args    : none
newcodeprevnextTop
 Title   : new
 Usage   : my $alignment = TFBS::Matrix::Alignment->new(%args)
 Function: constructor for the TFBS::Matrix::Alignment object
 Returns : a new TFBS::Matrix::Alignment object
 Args    : # you must specify:
 
	   -pfm1,      # a TFBS::Matrix::PFM object
	   -pfm2,      # another TFBS::Matrix::PFM object
            -binary,  # a valid path to the comparison algorithm (matrixalign)
	   
	   
	   #######
 
           -ext_penalty            #OPTIONAL gap extension penalty in Needleman-Wunsch
                                    algorithmstring. Default 0.01
           -open_penalty,          #OPTIONAL gap opening penalty in Needleman-Wunsch
                                    algorithmstring. Default 3.0
score(2)codeprevnextTop
 Title   : gaps
 Usage   : my $nr_of_gaps = $alignmentobject->gaps();
 Function: access the number of gaps in an alignment
 Returns : an integer
 Args    : none
strandcodeprevnextTop
 Title   : strand
 Usage   : my $strand = $alignmentobject->strand();
 Function: access the oriantation of the aligned patterns:
           ++= oriented as input
           +-= second pattern is reverse-complemented    
 Returns : a string
 Args    : none
Methods code
alignmentdescriptionprevnextTop
sub alignment {
return $_[0]->{'_align_string'};
}
gapsdescriptionprevnextTop
sub gaps {
return $_[0]->{'_gaps'};
}
lengthdescriptionprevnextTop
sub length {
return $_[0]->{'_aligned_positions'};
}
newdescriptionprevnextTop
sub new {
    #defines and createa an alignment
    # args: two pfm objects
    # binary file
    #optional scoring penalites
    my ($class, %args) = @_;
    my $self={
            _pfm1=> $args{'-pfm1'},
            _pfm2=> $args{'-pfm2'},
            _ext_penalty=>$args{'-ext_penalty'}|| 0.01,
            _open_penalty=> $args{'-open_penalty'}|| 3.00,
            _strand=>'',
            _align_string=>'',
            _gaps=>'',
            _aligned_positions =>'',
            _score=>'', 
             };
    
    bless $self, "TFBS::Matrix::Alignment";
    # errorcheck:
    
    
    
    # save temp files
    my($fh1, $file1) = tmpnam();
    print $fh1 $args{'-pfm1'}->rawprint()|| die " Cannot save temporary files for alignment";
    my($fh2, $file2) = tmpnam();
    print $fh2 $args{'-pfm2'}->rawprint()|| die " Cannot save temporary files for alignment";
 
    #align
    my @pfm1_string;
    my @pfm2_string;

    foreach (`$args{'-binary'} $file1 $file2 $self->{'_open_penalty'} $self->{'_ext_penalty'}`){
    # my @pfm2_string;
    my $max_length=$self->{'_pfm1'}->length();
    $max_length=$self->{'_pfm2'}->length() if ( $self->{'_pfm2'}->length() > $self->{'_pfm1'}->length());
    
     if (/^PFM1/){
        s/PFM1//;
        s/\t0/\t-/g;
        @pfm1_string= split();
        next;
     }
    if (/^PFM2/){
         s/PFM2//;
         s/\t0/\t-/g;
         @pfm2_string= split();
        next;
    }
    if (/^INFO/){
        my @temp=split;
        ($self->{'_score'},  $self->{'_strand'},  $self->{'_aligned_positions'}, $self->{'_gaps'})= ($temp[3], $temp[6], $temp[7],$temp[8]);
         next; 
     }
    }
    
    my $string= ($self->{'_pfm1'}->name()||$self->{'_pfm1'}->ID()||'PFM1')."\t\t";
    my $string2=($self->{'_pfm2'}->name()||$self->{'_pfm2'}->ID()||'PFM2')."\t\t";;
     if ($pfm1_string[0]==1){
         $string.="-\t" x ($pfm2_string[0]-1);
         foreach (my $j=1; $j< $pfm2_string[0]; $j++){
            $string2.="$j\t";
         }
     }
    if ($pfm2_string[0]==1){
        $string2.="-\t" x ($pfm1_string[0]-1);
        for (my $j=1; $j< $pfm1_string[0]; $j++){
           $string.="$j\t";
        }     
     }
     $string.= join("\t", @pfm1_string);
     $string2.= join("\t", @pfm2_string);
     
     if ($pfm1_string[-1]==$self->{'_pfm1'}->length()){
         $string.="\t-" x ($self->{'_pfm2'}->length()-$pfm2_string[-1]);
       for (my $j=$pfm2_string[-1]+1; $j<= $self->{'_pfm2'}->length(); $j++){
            $string2.="\t$j";
         }  
     }
     if ($pfm2_string[-1]==$self->{'_pfm2'}->length()){
         $string2.="\t-" x ($self->{'_pfm1'}->length()-$pfm1_string[-1]);
        for (my $j=$pfm1_string[-1]+1; $j<= $self->{'_pfm1'}->length(); $j++){
            $string.="\t$j";
         }
     }
     $self->{'_align_string'}= $string ."\n". $string2;
   
  return $self; 
}

# access functions
}
scoredescriptionprevnextTop
sub score {
return $_[0]->{'_score'};
}
stranddescriptionprevnextTop
sub strand {
return $_[0]->{'_strand'};
}
General documentation
FEEDBACKTop
Please send bug reports and other comments to the author.
AUTHOR - Boris LenhardTop
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.