Bio::SearchIO::Writer ResultTableWriter
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Summary
Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Package variables
Privates (from "my" definitions)
%column_map = ( 'query_name' => ['1', 'result', 'query_name', 's', 'QUERY' ], 'query_length' => ['2', 'result', 'query_length', 'd', 'LEN_Q'], 'query_description' => ['3', 'result', 'query_description', 's', 'DESC_Q'], 'num_hits' => ['4', 'result', 'num_hits', 'd', 'NUM_HITS'], )
Inherit
Bio::Root::Root Bio::SearchIO::SearchWriterI
Synopsis
    use Bio::SearchIO;
use Bio::SearchIO::Writer::ResultTableWriter;
my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::ResultTableWriter->new(); my $out = Bio::SearchIO->new( -writer => $writer ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); }
    use Bio::SearchIO;
use Bio::SearchIO::Writer::ResultTableWriter;
my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::ResultTableWriter->new( -columns => [qw( query_name query_length num_hits )] ); my $out = Bio::SearchIO->new( -writer => $writer, -file => ">result.out" ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); }
You can also specify different column labels if you don't want to use
the defaults. Do this by specifying a -labels hash reference
parameter when creating the ResultTableWriter object. The keys of the
hash should be the column number (left-most column = 1) for the label(s)
you want to specify. Here's an example:
    my $writer = Bio::SearchIO::Writer::ResultTableWriter->new( 
-columns => [qw( query_name
query_length
query_description
num_hits)],
-labels => { 1 => 'QUERY_GI',
2 => 'QUERY_LENGTH' } );
Description
Bio::SearchIO::Writer::ResultTableWriter outputs data in tab-delimited
format for each search result, one row per search result. This is a very
coarse-grain level of information since it only includes data
stored in the Bio::Search::Result::ResultI object itself and does not
include any information about hits or HSPs.
You most likely will never use this object but instead will use one of
its subclasses: Bio::SearchIO::Writer::HitTableWriter or
Bio::SearchIO::Writer::HSPTableWriter. Here are the columns that can be specified in the -columns
parameter when creating a ResultTableWriter object. If a -columns parameter
is not specified, this list, in this order, will be used as the default.
    query_name
query_length
query_description
For more details about these columns, see the documentation for the
corresponding method in Bio::Search::Result::ResultI.
Methods
column_map
No description
Code
new
No description
Code
_set_cols
No description
Code
_set_printf_fmt
No description
Code
_set_labels
No description
Code
_set_column_labels
No description
Code
_set_row_data_func
No description
Code
to_stringDescriptionCode
columns
No description
Code
column_labelsDescriptionCode
end_reportDescriptionCode
Methods description
to_string()code    nextTop
Note: this method is not intended for direct use. The
SearchIO::write_result() method calls it automatically if the writer
is hooked up to a SearchIO object as illustrated in the SYNOPSIS section .
 Title     : to_string()
:
Usage : print $writer->to_string( $result_obj, [$include_labels] );
:
Argument : $result_obj = A Bio::Search::Result::ResultI object
: $include_labels = boolean, if true column labels are included (default: false)
:
Returns : String containing tab-delimited set of data for each hit
: in a ResultI object. Some data is summed across multiple HSPs.
:
Throws : n/a
column_labelscodeprevnextTop
 Usage     : print $result_obj->column_labels();
Purpose : Get column labels for to_string().
Returns : String containing column labels. Tab-delimited.
Argument : n/a
Throws : n/a
end_reportcodeprevnextTop
 Title   : end_report
Usage : $self->end_report()
Function: The method to call when ending a report, this is
mostly for cleanup for formats which require you to
have something at the end of the document. Nothing for
a text message.
Returns : string
Args : none
Methods code
column_mapdescriptionprevnextTop
sub column_map {
 return %column_map
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_; 
    my $self = $class->SUPER::new(@args);

    my( $col_spec, $label_spec,
	$filters ) = $self->_rearrange( [qw(COLUMNS 
					    LABELS
					    FILTERS)], @args);
    
    $self->_set_cols( $col_spec );
    $self->_set_labels( $label_spec ) if $label_spec;
    $self->_set_printf_fmt();
    $self->_set_row_data_func();
    $self->_set_column_labels();
    
    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;
}


# Purpose : Stores the column spec internally. Also performs QC on the 
# user-supplied column specification.
#
}
_set_colsdescriptionprevnextTop
sub _set_cols {
    my ($self, $col_spec_ref) = @_;
    return if defined $self->{'_cols'};  # only set columns once
my %map = $self->column_map; if( not defined $col_spec_ref) { print STDERR "\nUsing default column map.\n"; $col_spec_ref = [ map { $_ } sort { $map{$a}->[0] <=> $map{$b}->[0] } keys %map ]; } if( ref($col_spec_ref) eq 'ARRAY') { # printf "%d columns to process\n", scalar(@$col_spec_ref);
my @col_spec = @{$col_spec_ref}; while( my $item = shift @col_spec ) { $item = lc($item); if( not defined ($map{$item}) ) { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Unknown column name: $item" ); } push @{$self->{'_cols'}}, $item; #print "pushing on to col $col_num, $inner: $item\n";
} } else { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Can't set columns: not a ARRAY ref", -value => $col_spec_ref ); }
}
_set_printf_fmtdescriptionprevnextTop
sub _set_printf_fmt {
    my ($self) = @_;

    my @cols = $self->columns();
    my %map = $self->column_map;

    my $printf_fmt = '';

    foreach my $col ( @cols ) {
	$printf_fmt .= "\%$map{$col}->[3]\t";
    }

    $printf_fmt =~ s/\\t$//;

    $self->{'_printf_fmt'} = $printf_fmt;
}
_set_labelsdescriptionprevnextTop
sub _set_labels {
    my ($self, $label_spec) = @_;
    if( ref($label_spec) eq 'HASH') {
        foreach my $col ( sort { $a <=> $b } keys %$label_spec ) {
#            print "LABEL: $col $label_spec->{$col}\n";
$self->{'_custom_labels'}->{$col} = $label_spec->{$col}; } } else { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Can't set labels: not a HASH ref: $label_spec" ); }
}
_set_column_labelsdescriptionprevnextTop
sub _set_column_labels {
    my $self = shift;

    my @cols = $self->columns;
    my %map = $self->column_map;
    my $printf_fmt = '';
    my (@data, $label, @underbars);

    my $i = 0;
    foreach my $col( @cols ) {
	$i++;
        $printf_fmt .= "\%s\t";

        if(defined $self->{'_custom_labels'}->{$i}) {
	    $label = $self->{'_custom_labels'}->{$i};
        }
	else {
	    $label = $map{$col}->[4];
	}
	push @data, $label;
        push @underbars, '-' x length($label);

    }
    $printf_fmt =~ s/\\t$//;

    my $str = sprintf "$printf_fmt\n", @data;

    $str =~ s/\t\n/\n/;
    $str .= sprintf "$printf_fmt\n", @underbars;

    $str =~ s/\t\n/\n/gs;
    $self->{'_column_labels'} = $str;
}

# Purpose : Generate a function that will call the appropriate
# methods on the result, hit, and hsp objects to retrieve the column data
# specified in the column spec.
#
# We should only have to go through the column spec once
# for a given ResultTableWriter. To permit this, we'll generate code
# for a method that returns an array of the data for a row of output
# given a result, hit, and hsp object as arguments.
#
}
_set_row_data_funcdescriptionprevnextTop
sub _set_row_data_func {
    my $self = shift;

    # Now we need to generate a string that can be eval'd to get the data.
my @cols = $self->columns(); my %map = $self->column_map; my @data; while( my $col = shift @cols ) { my $object = $map{$col}->[1]; my $method = $map{$col}->[2]; my $arg = ''; if( $method =~ m!(\w+)/(\w+)! ) {
$method = $1;
$arg = "\"$2\""; } push @data, "\$$object->$method($arg)"; } my $code = join( ",", @data); if( $self->verbose > 0 ) { ## Begin Debugging
$self->debug( "Data to print:\n"); foreach( 0..$#data) { $self->debug( " [". ($_+ 1) . "] $data[$_]\n");} $self->debug( "CODE:\n$code\n"); $self->debug("Printf format: ". $self->printf_fmt. "\n"); ## End Debugging
} my $func = sub { my ($result, $hit, $hsp) = @_; my @r = eval $code; # This should reduce the occurrence of those opaque "all zeros" bugs.
if( $@ ) { $self->throw("Trouble in ResultTableWriter::_set_row_data_func() eval: $@\n\n"); } return @r; }; $self->{'_row_data_func'} = $func;
}
to_stringdescriptionprevnextTop
sub to_string {
#----------------
my ($self, $result, $include_labels) = @_; my $str = $include_labels ? $self->column_labels() : ''; my $resultfilter = $self->filter('RESULT'); if( ! defined $resultfilter || &{$resultfilter}($result) ) { my @row_data = &{$self->{'_row_data_func'}}( $result ); $str .= sprintf "$self->{'_printf_fmt'}\n", @row_data; $str =~ s/\t\n/\n/gs; } return $str;
}
columnsdescriptionprevnextTop
sub columns {
    my $self = shift;
    my @cols;
    if( ref $self->{'_cols'} ) {
        @cols = @{$self->{'_cols'}};
    }
    else {
        my %map = $self->column_map;
        @cols = sort { $map{$a}->[0] <=> $map{$b}->[0] } keys %map;
   }
    return @cols;
}
column_labelsdescriptionprevnextTop
sub column_labels {
 shift->{'_column_labels'}
}
end_reportdescriptionprevnextTop
sub end_report {
    return '';
}
General documentation
FEEDBACKTop
Mailing Lists Top
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR Top
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports
and comments.
COPYRIGHTTop
Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
Bio::SearchIO::Writer::HitTableWriter,
Bio::SearchIO::Writer::HSPTableWriter
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