NAME¶
Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each
Bio::Search::Result::ResultI object.
SYNOPSIS¶
Example 1: Using the default columns¶
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) );
}
Example 2: Specifying a subset of columns¶
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) );
}
Custom Labels¶
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.
Available Columns¶
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.
FEEDBACK¶
Mailing Lists¶
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¶
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 Bugs¶
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://github.com/bioperl/bioperl-live/issues
AUTHOR¶
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
COPYRIGHT¶
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.
DISCLAIMER¶
This software is provided "as is" without warranty of any kind.
SEE ALSO¶
Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::HSPTableWriter
METHODS¶
to_string()¶
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_labels¶
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_report¶
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
filter¶
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