Bio::Matrix::IO scoring
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies
Package variables
No package variables defined.
Included modules
Bio::Matrix::Scoring
Inherit
Bio::Matrix::IO
Synopsis
  use Bio::Matrix::IO;
  my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                   -file   => 'BLOSUM50');
  my $matrix = $parser->next_matrix;
Description
Describe the object here
Methods
next_matrixDescriptionCode
write_matrixDescriptionCode
Methods description
next_matrixcode    nextTop
 Title   : next_matrix
 Usage   : my $matrux = $parser->next_matrix
 Function: parses a scoring matrix (BLOSUM,PAM styles) 
 Returns : Bio::Matrix::Scoring
 Args    : none
write_matrixcodeprevnextTop
 Title   : write_matrix
 Usage   : $matio->write_matrix($matrix)
 Function: Write out a matrix in the BLOSUM/PAM format
 Returns : none
 Args    : Bio::Matrix::Scoring
Methods code
next_matrixdescriptionprevnextTop
sub next_matrix {
   my ($self) = @_;
   local ($_);
   my (@matrix,@cols,@rows,%extras,$inmatrix);
   while( defined ( $_ = $self->_readline ) ) {
       next if ( /^\s*$/);
       if( /^\#/ ) {
	   if( $inmatrix ) { 
	       $self->_pushback($_);
	       last;
	   }
	   if( m/Entropy\s+\=\s+(\S+)\,\s+
	       Expected\s+\=\s+(\S+)/ox ) {
	       $extras{'-entropy'} = $1;
	       $extras{'-expected'} = $2;
	   } elsif ( m/Expected\s+score\s+\=\s+(\S+)\,
		     \s+Entropy\s+\=\s+(\S+)/xo ){
	       $extras{'-entropy'} = $2;
	       $extras{'-expected'} = $1;
	   } elsif( m/(PAM\s+\d+)\s+substitution.+
		    scale\s+\=\s+(\S+)\s+\=\s+(\S+)/ox ) {
	       $extras{'-matrix_name'} = $1;
	       $extras{'-scale'}       = $2;	       
	       $extras{'-scale_value'} = $3;
	   } elsif( /Blocks Database\s+\=\s+(\S+)/o ) {
	       $extras{'-database'} = $1;
	   } elsif( m/(\S+)\s+Bit\s+Units/ox ) {
	       $extras{'-scale'} = $1;
	   } elsif( m/Lowest score\s+\=\s+(\S+)\,\s+
		    Highest score\s+\=\s+(\S+)/ox ) {
	       $extras{'-lowest_score'} = $1;
	       $extras{'-highest_score'} = $2;
	   } elsif( m/(Lambda)\s+\=\s+(\S+)\s+bits\,
		    \s+(H)\s+\=\s+(\S+)/ox ) {
	       # This is a DNA matrix
	       $extras{$1} = $2;
	       $extras{$3} = $4;
	   }	       
       } elsif( s/^\s+(\S+)/$1/ ) {
	   @cols = split;
	   if( $cols[0] ne 'A' ) {
	       $self->warn("Unrecognized first line of matrix, we might not have parsed it correctly");
	   }
	   $inmatrix = 1;
       } elsif( $inmatrix ) {
	   if( ! /^(\S+)/ ) { $inmatrix = 0; next }
	   my ($rowname,@row) = split;
	   push @rows, $rowname;
	   push @matrix, [@row];
       } else { 
	   print;
       }
   }
   my $matrix = Bio::Matrix::Scoring->new(-values     =>\@ matrix,
					 -rownames   =>\@ rows,
					 -colnames   =>\@ cols,
					 %extras);
}
write_matrixdescriptionprevnextTop
sub write_matrix {
   my ($self,@args) = @_;
   $self->warn("cannot actually use this function yet - it isn't finished");
   return;
}


1;
}
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/wiki/Mailing_lists  - 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
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : my $obj = Bio::Matrix::IO::scoring->new();
 Function: Builds a new Bio::Matrix::IO::scoring object 
 Returns : an instance of Bio::Matrix::IO::scoring
 Args    :