Bio::SearchIO::Writer TextResultWriter
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text.
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::SearchIO::SearchWriterI
POSIX
Inherit
Bio::Root::Root Bio::SearchIO::SearchWriterI
Synopsis
  use Bio::SearchIO;
  use Bio::SearchIO::Writer::TextResultWriter;

  my $in = new Bio::SearchIO(-format => 'blast',
			     -file   => shift @ARGV);

  my $writer = new Bio::SearchIO::Writer::TextResultWriter();
  my $out = new Bio::SearchIO(-writer => $writer);
  $out->write_result($in->next_result);
Description
This object implements the SearchWriterI interface which will produce
a set of Text for a specific Bio::Search::Report::ReportI interface.
Methods
BEGIN Code
newDescriptionCode
to_stringDescriptionCode
id_parserDescriptionCode
default_id_parserDescriptionCode
MIN
No description
Code
MAX
No description
Code
algorithm_referenceDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::SearchIO::Writer::TextResultWriter();
 Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
 Returns : Bio::SearchIO::Writer::TextResultWriter
 Args    :
to_stringcodeprevnextTop
 Purpose   : Produces data for each Search::Result::ResultI in a string.
           : This is an abstract method. For some useful implementations,
           : see ResultTableWriter.pm, HitTableWriter.pm, 
           : and HSPTableWriter.pm.
 Usage     : print $writer->to_string( $result_obj, @args );
 Argument  : $result_obj = A Bio::Search::Result::ResultI object
           : @args = any additional arguments used by your implementation.
 Returns   : String containing data for each search Result or any of its
           : sub-objects (Hits and HSPs).
 Throws    : n/a
id_parsercodeprevnextTop
  Title   : id_parser
  Usage   : $index->id_parser( CODE )
  Function: Stores or returns the code used by record_id to
            parse the ID for record from a string.  Useful
            for (for instance) specifying a different
            parser for different flavours of FASTA file. 
            Returns \&default_id_parser (see below) if not
            set. If you supply your own id_parser
            subroutine, then it should expect a fasta
            description line.  An entry will be added to
            the index for each string in the list returned.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE
default_id_parsercodeprevnextTop
  Title   : default_id_parser
  Usage   : $id = default_id_parser( $header )
  Function: The default Fasta ID parser for Fasta.pm
            Returns $1 from applying the regexp /^>\s*(\S+)/
            to $header.
  Returns : ID string
  Args    : a fasta header line string
algorithm_referencecodeprevnextTop
 Title   : algorithm_reference
 Usage   : my $reference = $writer->algorithm_reference($result);
 Function: Returns the appropriate Bibliographic reference for the 
           algorithm format being produced
 Returns : String
 Args    : Bio::Search::Result::ResultI to reference
Methods code
BEGINTop
BEGIN {
    $MaxDescLen = 65;
    $AlignmentLineWidth = 60;
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($filters) = $self->_rearrange([qw(FILTERS)],@args);
  if( defined $filters ) {
      if( !ref($filters) =~ /HASH/i ) { 
	  $self->warn("Did not provide a hashref for the FILTERS option, ignoring.");
      } else { 
	  while( my ($type,$code) = each %{$filters} ) {
	      $self->filter($type,$code);
	  }
      }
  }

  return $self;
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self,$result) = @_; 
    return '' unless defined $result;
    my ($resultfilter,$hitfilter,
	$hspfilter) = ( $self->filter('RESULT'),
			$self->filter('HIT'),
			$self->filter('HSP'));
    return '' if( defined $resultfilter && ! &{$resultfilter}($result) );
    
    my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE';
    my $str = sprintf(
qq{%s %s 

Bioperl Reformatted BLAST Format report of %s Search output 
with Bio::SearchIO Bioperl Reformatted BLAST Format Module %s

%s

Query=%s %s 
         (%d letters)

Database: %s 
          %d sequences; %d total letters

Sequences producing significant alignments:         Score       E
                                                    (bits)    value
},
		      $result->algorithm,  $result->algorithm_version,
		      $result->algorithm, ref($result),
		      $result->program_reference() || $self->algorithm_reference($result),
		      $result->query_name, $result->query_description, 
		      $result->query_length, 
		      $result->database_name(),
		      $result->database_entries(),
		      $result->database_letters(),
		      );
    my $hspstr = '';
    $result->rewind();
    while( my $hit = $result->next_hit ) {
	next if( defined $hitfilter && ! &{$hitfilter}($hit) );
	my $nm = $hit->name();
	my $id_parser = $self->id_parser;
	print STDERR "no $nm for name (",$hit->description(), ")\n" unless $nm;
	my ($gi,$acc) = &$id_parser($nm);
	my $p = "%-".$MaxDescLen. "s";
	my $descsub = $hit->name . " " . $hit->description;
	if( length($descsub) > ($MaxDescLen) ) {
	    $descsub = substr($descsub,0,$MaxDescLen-3) . "...";
	}

	$str .= sprintf("$p   %s %-4s  %s\n",
			$descsub,
			defined $hit->raw_score ? $hit->raw_score : ' ',
			defined $hit->significance ? $hit->significance : '?');

	$hspstr .= sprintf(">%s %s\n%9sLength = %d\n\n",
			   $hit->name, 
			   defined $hit->description ? $hit->description : '', 
			   '', # empty is for the %9s in the str formatting 
			   $hit->length);
	$hit->rewind(); # make sure we are at the beginning of the list
	while( my $hsp = $hit->next_hsp ) {
	    next if( defined $hspfilter && ! &{$hspfilter}($hsp) );
	    $hspstr .= sprintf(" Score = %4s bits (%s), Expect = %s",
			       $hsp->bits, $hsp->score, $hsp->evalue);
	    if( $hsp->pvalue ) {
		$hspstr .= ", P = ".$hsp->pvalue;
	    }
	    $hspstr .= "\n";
	    $hspstr .= sprintf(" Identities = %d/%d (%d%%)",
			         ( $hsp->frac_identical('total') * 
				   $hsp->length('total')),
			       $hsp->length('total'),
			     POSIX::floor($hsp->frac_identical('total') * 100));

	    if( $hit->algorithm =~ /(T)?BLAST(X|P)/ ||
		$hit->algorithm =~ /(T)?FAST(X|Y|P)/ ||
		$hit->algorithm eq 'TBLASTN' ||
		$hit->algorithm eq 'TFASTN' 
		) {
		$hspstr .= sprintf(", Positives = %d/%d (%d%%)",
				   ( $hsp->frac_conserved('total') * 
				     $hsp->length('total')),
				   $hsp->length('total'),
				   POSIX::floor($hsp->frac_conserved('total') * 100));
		
	    }
	    if( $hsp->gaps ) {
		$hspstr .= sprintf(", Gaps = %d/%d (%d%%)\n",
				   $hsp->gaps('total'),
				   $hsp->length('total'),
				   POSIX::floor(100 * $hsp->gaps('total') / 
					       $hsp->length('total')));
	    }
	    
	    my ($h,$q) = ( $hsp->hit->frame ,$hsp->query->frame);
		
	    if( $h || $q ) {
		$hspstr .= " Frame = ";
		
		if( $h && ! $q) {  $hspstr .= $h }
		elsif( $q && ! $h) {  $hspstr .= $q }
		else { 
		    $hspstr .= " $h / $q\n ";
		}
	    }
	    $hspstr .= "\n";
	    
	    my @hspvals = ( {'name' => 'Query:',
			     'seq'  => $hsp->query_string,
			     'start' => $hsp->query->strand >= 0 ? 
				 $hsp->query->start : $hsp->query->end,
			     'end'   => $hsp->query->strand >= 0 ? 
				  $hsp->query->end : $hsp->query->start,
			     'index' => 0,
			     'direction' => $hsp->query->strand || 1
			     },
			    { 'name' => ' 'x6,
			      'seq'  => $hsp->homology_string,
			      'start' => undef,
			      'end'   => undef,
			      'index' => 0,
			      'direction' => 1
			      },
			    { 'name'  => 'Sbjct:',
			      'seq'   => $hsp->hit_string,
			      'start' => $hsp->hit->strand >= 0 ? $hsp->hit->start : $hsp->hit->end,
			      'end'   => $hsp->hit->strand >= 0 ? $hsp->hit->end : $hsp->hit->start,
			      'index' => 0,
			      'direction' => $hsp->query->strand || 1
			      }
			    );	    
	    
	    
	    # let's set the expected length (in chars) of the starting number
	    # in an alignment block so we can have things line up
	    # Just going to try and set to the largest
	    
	    my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}),
						length($hspvals[0]->{'end'}),
						length($hspvals[2]->{'start'}),
						length($hspvals[2]->{'end'}));
	    my $count = 0;
	    while ( $count <= $hsp->length('total') ) {
		foreach my $v ( @hspvals ) {
		    my $piece = substr($v->{'seq'}, $v->{'index'} +$count,
				       $AlignmentLineWidth);
		    my $cp = $piece;
		    my $plen = scalar ( $cp =~ tr/\-//);
		    my ($start,$end) = ('','');
		    if( defined $v->{'start'} ) { 
			$start = $v->{'start'};
			# since strand can be + or - use the direction
			# to signify which whether to add or substract from end
			my $d = ( ( $v->{'direction'} ) * 
				  ( $AlignmentLineWidth - $plen ));
			if( length($piece) < $AlignmentLineWidth ) {
			    $d = (length($piece) - $plen) * $v->{'direction'};
			}
			$end   = $v->{'start'} + $d - 1;


			$v->{'start'} += $d;
		    }
		    $hspstr .= sprintf("%s %-".$numwidth."s %s %s\n",
				       $v->{'name'},
				       $start,
				       $piece,
				       $end
				       );
		}
		$count += $AlignmentLineWidth;
		$hspstr .= "\n";
	    }
	}
	$hspstr .= "\n";
    }
    $str .= "\n\n".$hspstr;

    foreach my $param ( $result->available_parameters ) {
	$str .= "$param: ". $result->get_parameter($param) ."\n";
	
    }
    $str .= "Search Statistics\n";

   foreach my $stat ( sort $result->available_statistics ) {
	$str .= "$stat: ". $result->get_statistic($stat). "\n";
    }
    $str .=  "\n\n";
    return $str;
}
id_parserdescriptionprevnextTop
sub id_parser {
    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;
}
default_id_parserdescriptionprevnextTop
sub default_id_parser {
        my ($string) = @_;
    my ($gi,$acc);
    if( $string =~ s/gi\|(\d+)\|?// ) 
    { $gi = $1; $acc = $1;}
    
    if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) {
	$acc = defined $2 ? $2 : $1;
    } else {
        $acc = $string;
	$acc =~ s/^\s+(\S+)/$1/;
	$acc =~ s/(\S+)\s+$/$1/;	
    } 
    return ($gi,$acc);
}
MINdescriptionprevnextTop
sub MIN {
 $a <=> $b ? $a : $b;
}
MAXdescriptionprevnextTop
sub MAX {
 $a <=> $b ? $b : $a;
}
algorithm_referencedescriptionprevnextTop
sub algorithm_reference {
   my ($self,$result) = @_;
   return '' if( ! defined $result || !ref($result) ||
		 ! $result->isa('Bio::Search::Result::ResultI')) ;   
   if( $result->algorithm =~ /BLAST/i ) {
       my $res = $result->algorithm . ' '. $result->algorithm_version. "\n";
       if( $result->algorithm_version =~ /WashU/i ) {
	   return $res .qq{
Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.
 
Reference:  Gish, W. (1996-2000) http://blast.wustl.edu
};	   
       } else {
	   return $res . qq{
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
};
       }       
   } elsif( $result->algorithm =~ /FAST/i ) {
       return $result->algorithm. " ". $result->algorithm_version . "\n".
	   "\nReference: Pearson et al, Genomics (1997) 46:24-36\n";
   } else { 
       return '';
   }
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
filterTop
 Title   : filter
 Usage   : $writer->filter('hsp', \&hsp_filter);
 Function: Filter out either at HSP,Hit,or Result level
 Returns : none
 Args    : string => data type,
           CODE reference