bio::searchio::writer::bsmlresultwriter(3pm) [debian man page]
Bio::SearchIO::Writer::BSMLResultWriter(3pm) User Contributed Perl Documentation Bio::SearchIO::Writer::BSMLResultWriter(3pm)NAME
Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer
SYNOPSIS
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-file => 'result.blast',
-format => 'blast');
my $out = Bio::SearchIO->new(-output_format => 'BSMLResultWriter',
-file => ">result.bsml");
while( my $r = $in->next_result ) {
$out->write_result($r);
}
DESCRIPTION
This is a writer to produce BSML for a search result.
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 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
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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::Writer::BSMLResultWriter->new();
Function: Builds a new Bio::SearchIO::Writer::BSMLResultWriter object
Returns : an instance of Bio::SearchIO::Writer::BSMLResultWriter
Args :
to_string
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
perl v5.14.2 2012-03-02 Bio::SearchIO::Writer::BSMLResultWriter(3pm)
Check Out this Related Man Page
Bio::SearchIO::Writer::ResultTableWriter(3pm) User Contributed Perl Documentation Bio::SearchIO::Writer::ResultTableWriter(3pm)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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::SearchIO::Writer::ResultTableWriter(3pm)