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Summary

Bio::Tools::Run::Alignment::DBA - Object for the alignment of two
sequences using the DNA Block Aligner program.

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

  use Bio::Tools::Run::Alignment::DBA;

  #  Build a dba alignment factory
  my @params = ('matchA' => 0.75, 
                 'matchB' => '0.55',
                 'dymem' =>'linear');
  my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);

  #  Pass the factory a filename with 2 sequences to be aligned.
  $inputfilename = 't/data/dbaseq.fa';
  # @hsps is an array of GenericHSP objects
  my @hsps = $factory->align($inputfilename); 

  # or
  my @files = ('t/data/dbaseq1.fa','t/data/dbaseq2.fa');
  my @hsps = $factory->align(\@files);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  my @hsps = $factory->align($seq_array_ref);

Description

DNA Block Aligner program (DBA) was developed by Ewan Birney. DBA
is part of the Wise package available at
http://www.sanger.ac.uk/software/wise2.
You will need to enable dba to find the dba program. This can
be done in a few different ways:
1. Define an environmental variable WISEDIR:

  export WISEDIR =/usr/local/share/wise2.2.0

2. Include a definition of an environmental variable WISEDIR in
every script that will use DBA.pm:

  $ENV{WISEDIR} = '/usr/local/share/wise2.2.20';

3. Make sure that the dba application is in your PATH.

Methods

Methods description

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

 Title   : align
 Usage   :
            $inputfilename = 't/data/seq.fa';
            @hsps = $factory->align($inputfilename);
          or
            #@seq_array is array of Seq objs
            $seq_array_ref = \@seq_array; 
            @hsps = $factory->align($seq_array_ref);
          or
            my @files = ('t/data/seq1.fa','t/data/seq2.fa');
            @hsps = $factory->align(\@files);
 Function: Perform a DBA  alignment

 Returns : An array of Bio::Search::HSP::GenericHSP objects 
 Args    : Name of a file containing a set of 2 fasta sequences
           or else a reference to an array  to 2  Bio::Seq objects.
           or else a reference to an array of 2 file
              names containing 1 fasta sequence each

 Throws an exception if argument is not either a string (eg a
 filename) or a reference to an array of 2 Bio::Seq objects.  If
 argument is string, throws exception if file corresponding to string
 name can not be found. If argument is Bio::Seq array, throws
 exception if less than two sequence objects are in array.

 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:   makes actual system call to dba program
 Example :
 Returns : nothing; dba  output is written to a temp file
 Args    : Name of a file containing a set of unaligned fasta sequences
           and hash of parameters to be passed to dba

 Title   :  __parse_results
 Usage   :  Internal function, not to be called directly
 Function:  Parses dba output 
 Example :
 Returns : an reference to an array of GenericHSPs
 Args    : the name of the output file

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:   Create input file for dba program
 Example :
 Returns : name of file containing dba data input
 Args    : Seq or Align object reference or input file name

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:   Create parameter inputs for dba program
 Example :
 Returns : parameter string to be passed to dba 
           during align or profile_align
 Args    : name of calling object

 Title   :  _query_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the query sequence 
 Example :
 Returns : 
 Args    :

 Title   :  _subject_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the subject sequence
 Example :
 Returns :

 Args    :

Methods code

BEGIN {

    @DBA_PARAMS = qw(MATCHA MATCHB MATCHC MATCHD GAP BLOCKOPEN UMATCH SINGLE 
                     NOMATCHN PARAMS KBYTE DYMEM DYDEBUG ERRORLOG);
    @OTHER_SWITCHES = qw(OUTFILE);
    @DBA_SWITCHES = qw(HELP SILENT QUIET ERROROFFSTD ALIGN LABEL); 

    # Authorize attribute fields
    foreach my $attr ( @DBA_PARAMS, @DBA_SWITCHES,
                       @OTHER_SWITCHES) { $OK_FIELD{$attr}++;

}

sub program_name {

  return 'dba';

}

sub program_dir {

  return Bio::Root::IO->catfile($ENV{WISEDIR},"/src/bin") if $ENV{WISEDIR};

}

sub new {

  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);

  my ($attr, $value);

  while (@args) {
    $attr =   shift @args;
    $value =  shift @args;
    next if( $attr =~ /^-/ ); # don't want named parameters
    if ($attr =~/'PROGRAM'/i )  {
      $self->executable($value);
      next;
    }
    $self->$attr($value);
  }
  return $self;

}

sub AUTOLOAD {

    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};

}

sub version {

    my ($self) = @_;

    my $exe = $self->executable();
    return undef unless defined $exe;
    my $string = `$exe -- ` ;
    $string =~ /\(([\d.]+)\)/;
    return $1 || undef;

}

sub align {

    my ($self,$input) = @_;
    my ($temp,$infile1, $infile2, $seq);
    my ($attr, $value, $switch);

# Create input file pointer
    ($infile1,$infile2)= $self->_setinput($input);
    if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 sequences in $input !");}

# Create parameter string to pass to dba program
    my $param_string = $self->_setparams();

# run dba 
    my @hsps = $self->_run($infile1,$infile2,$param_string);
    return @hsps;
}

#################################################

}

sub _run {

    my ($self,$infile1,$infile2,$param_string) = @_;
    my $instring;
    $self->debug( "Program ".$self->executable."\n");
    unless( $self->outfile){
	  my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir);
    close($tfh);
  	undef $tfh;
  	$self->outfile($outfile);
    }
    my $outfile = $self->outfile(); 
    my $commandstring = $self->executable." $param_string -pff $infile1 $infile2 > $outfile";
    $self->debug( "dba command = $commandstring");
    my $status = system($commandstring);
    $self->throw( "DBA call ($commandstring) crashed: $?\n ") unless $status==0;
    #parse pff format and return a Bio::Search::HSP::GenericHSP array
    my $hsps   = $self->_parse_results($outfile);

    return @{$hsps};

}

sub _parse_results {

    my ($self,$outfile) = @_;
    $outfile||$self->throw("No outfile specified");
    my ($start,$end,$name,$seqname,$seq,$seqchar,$tempname,%align);
    my $count = 0;
    my @hsps;
    open(OUT,$outfile);
    my (%query,%subject);
    while(my $entry = <OUT>){
      if($entry =~ /^>(.+)/ ) {
        $tempname = $1;
        if( defined $name ) {
          if($count == 0){
            my @parse = split("\t",$name);
            $query{seqname}  = $parse[0];
            $query{start}    = $parse[3];
            $query{end}      = $parse[4];
            $query{score}    = $parse[5];
            $query{strand}   = ($parse[6] eq '+') ? 1 : -1;
            my @tags         = split(";",$parse[8]);
            foreach my $tag(@tags){
              $tag =~/(\S+)\s+(\S+)/;
              $query{$1} = $2;
            }
            $query{seq}      = $seqchar;
            $count++;
          }
          elsif ($count == 1){
            my @parse = split("\t",$name);
            $subject{seqname}  = $parse[0];
            $subject{start}    = $parse[3];
            $subject{end}      = $parse[4];
            $subject{score}    = $parse[5];
            $subject{strand}   = ($parse[6] eq '+') ? 1:-1;
            my @tags         = split(";",$parse[8]);
            foreach my $tag(@tags){
              $tag =~/(\S+)\s+(\S+)/;
              $subject{$1} = $2;
            }
            $subject{seq}   = $seqchar;
            #create homology string
            my $xor = $query{seq}^$subject{seq};
            my $identical = $xor=~tr/\c@/*/;
            $xor=~tr/*/ /c;
            my $hsp= Bio::Search::HSP::GenericHSP->new(-algorithm     =>'DBA',
                                                       -score         =>$query{score},
                                                       -hsp_length    =>length($query{seq}),
                                                       -query_gaps    =>$query{gaps},
                                                       -hit_gaps      =>$subject{gaps}, 
                                                       -query_name    =>$query{seqname},
                                                       -query_start   =>$query{start}, 
                                                       -query_end     =>$query{end},
                                                       -hit_name      =>$subject{seqname},
                                                       -hit_start     =>$subject{start}, 
                                                       -hit_end       =>$subject{end},
                                                       -hit_length    =>length($self->_subject_seq->seq),
                                                       -query_length  =>length($self->_query_seq->seq),
                                                       -query_seq     =>$query{seq},
                                                       -hit_seq       =>$subject{seq},
                                                       -conserved     =>$identical,
                                                       -identical   =>$identical,
                                                       -homology_seq  =>$xor);
            push @hsps, $hsp; 
            $count  = 0;
          }
      }
          $name = $tempname;
          $seqchar  = "";
          next;
      }
      $entry =~ s/[^A-Za-z\.\-]//g;
      $seqchar .= $entry;
  }
  #do for the last entry
  if($count == 1){
    my @parse = split("\t",$name);
    $subject{seqname}  = $parse[1];
    $subject{start}    = $parse[3];
    $subject{end}      = $parse[4];
    $subject{score}    = $parse[5];
    $subject{strand}   = ($parse[6] eq '+') ? 1:-1;
    my @tags         = split(";",$parse[8]);
    foreach my $tag(@tags){
      $tag =~/(\S+)\s+(\S+)/;
      $subject{$1} = $2;
    }
    $subject{seq}   = $seqchar;

    #create homology string
    
    my $xor = $query{seq}^$subject{seq};
    my $identical = $xor=~tr/\c@/*/;
    $xor=~tr/*/ /c;
    my $hsp= Bio::Search::HSP::GenericHSP->new(-algorithm     =>'DBA',
                                               -score         =>$query{score},
                                               -hsp_length    =>length($query{seq}),
                                               -query_gaps    =>$query{gaps},
                                               -hit_gaps      =>$subject{gaps},
                                               -query_name    =>$query{seqname},
                                               -query_start   =>$query{start},
                                               -query_end     =>$query{end},
                                               -hit_name      =>$subject{seqname},
                                               -hit_start     =>$subject{start},
                                               -hit_end       =>$subject{end},
                                               -hit_length    =>length($self->_subject_seq->seq),
                                               -query_length  =>length($self->_query_seq->seq),
                                               -query_seq     =>$query{seq},
                                               -hit_seq       =>$subject{seq},
                                               -conserved     =>$identical,
                                               -identical     =>$identical,
                                               -homology_seq  =>$xor);
     push @hsps, $hsp;
  }


  return\@ hsps;

}

sub _setinput {

  my ($self, $input, $suffix) = @_;
  my ($infilename, $seq, $temp, $tfh1,$tfh2,$outfile1,$outfile2);

  #there is gotta be some repetition here...need to clean up

  if (ref($input) ne "ARRAY"){ #a single file containg 2 seqeunces
    $infilename = $input;
    unless(-e $input){return 0;}
    my  $in  = Bio::SeqIO->new(-file => $infilename , '-format' => 'Fasta');
    ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
    ($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
    
    my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'Fasta','-flush'=>1);
    my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'Fasta','-flush'=>1);

    my $seq1 = $in->next_seq() || return 0; 
    my $seq2 = $in->next_seq() || return 0; 
    $out1->write_seq($seq1);
    $out2->write_seq($seq2);
    $self->_query_seq($seq1);
    $self->_subject_seq($seq2);
    $out1->close();
    $out2->close();
    close($tfh1);
    close($tfh2);
    undef $tfh1;
    undef $tfh2;
    return $outfile1,$outfile2;
  }
  else {
    scalar(@{$input}) == 2 || $self->throw("dba alignment can only be run  on 2 sequences not.");
    if(ref($input->[0]) eq ""){#passing in two file names
      my $in1  = Bio::SeqIO->new(-file => $input->[0], '-format' => 'fasta');
      my $in2  = Bio::SeqIO->new(-file => $input->[1], '-format' => 'fasta');

      ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
      ($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);

      my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
      my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'fasta');

      my $seq1 = $in1->next_seq() || return 0; 
      my $seq2 = $in2->next_seq() || return 0; 
      $out1->write_seq($seq1);
      $out2->write_seq($seq2);
      $self->_query_seq($seq1);
      $self->_subject_seq($seq2);
      close($tfh1);
      close($tfh2);
      undef $tfh1;
      undef $tfh2;
      return $outfile1,$outfile2;
    }
    elsif($input->[0]->isa("Bio::PrimarySeqI") && $input->[1]->isa("Bio::PrimarySeqI")) {
      ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
      ($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);

      my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
      my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'fasta');

      $out1->write_seq($input->[0]);
      $out2->write_seq($input->[1]);
      $self->_query_seq($input->[0]);
      $self->_subject_seq($input->[1]);

      close($tfh1);
      close($tfh2);
      undef $tfh1;
      undef $tfh2;
      return $outfile1,$outfile2;
    }  
    else {
       return 0;
    }
  }
  return 0;

}

sub _setparams {

    my ($attr, $value, $self);

    $self = shift;

    my $param_string = "";
    for  $attr ( @DBA_PARAMS ) {
	$value = $self->$attr();
	next unless (defined $value);
#      next if $attr =~/outfile/i;

	my $attr_key = lc $attr; #put params in format expected by dba 
	if($attr_key =~ /match([ABCDabcd])/i){
	    $attr_key = "match".uc($1);
	}
	$attr_key = ' -'.$attr_key;
	$param_string .= $attr_key.' '.$value;
    }
    for  $attr ( @DBA_SWITCHES) {
	$value = $self->$attr();
	next unless ($value);
	my $attr_key = lc $attr; #put switches in format expected by dba 
	$attr_key = ' -'.$attr_key;
	$param_string .= $attr_key ;
    }
    return $param_string;

}

sub _query_seq {

  my ($self,$seq) = @_;
  if(defined $seq){
    $self->{'_query_seq'} = $seq;
  }
  return $self->{'_query_seq'};

}

sub _subject_seq {

  my ($self,$seq) = @_;
  if(defined $seq){
    $self->{'_subject_seq'} = $seq;
  }
  return $self->{'_subject_seq'};
}
1; # Needed to keep compiler happy

}

General documentation

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rather than to the module maintainer directly. Many experienced and
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with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _