Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text. 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); This object implements the SearchWriterI interface which will produce a set of Text for a specific Bio::Search::Report::ReportI interface. You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %hash is an associative array which contains any or all of the keys (HSP, HIT, RESULT). The values pointed to by these keys would be references to a subroutine which expects to be passed an object - one of Bio::Search::HSP::HSPI, Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively. Each function needs to return a boolean value as to whether or not the passed element should be included in the output report - true if it is to be included, false if it to be omitted. For example to filter on sequences in the database which are too short for your criteria you would do the following. Define a hit filter method sub hit_filter { my $hit = shift; return $hit->length E<gt> 100; # test if length of the hit sequence # long enough } my $writer = new Bio::SearchIO::Writer::TextResultWriter( -filters => { 'HIT' =E<gt> \&hit_filter } ); Another example would be to filter HSPs on percent identity, let's only include HSPs which are 75% identical or better. sub hsp_filter { my $hsp = shift; return $hsp->percent_identity E<gt> 75; } my $writer = new Bio::SearchIO::Writer::TextResultWriter( -filters => { 'HSP' =E<gt> \&hsp_filter } ); See Bio::SearchIO::SearchWriterI for more info on the filter method. This module will use the module Text::Wrap if it is installed to wrap the Query description line. If you do not have Text::Wrap installed this module will work fine but you won't have the Query line wrapped. You will see a warning about this when you first instantiate a TextResultWriter - to avoid these warnings from showing up, simply set the verbosity upon initialization to -1 like this: my $writer = new Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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 : -filters => hashref with any or all of the keys (HSP HIT RESULT) which have values pointing to a subroutine reference which will expect to get a Hit,HSP, Result object respectively -no_wublastlinks => boolean. Do not display WU-BLAST lines even if they are parsed out Links = (1)

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

start_report
Title : start_report Usage : $index->start_report( CODE ) Function: Stores or returns the code to write the start of the <HTML> block, the <TITLE> block and the start of the <BODY> block of HTML. Useful for (for instance) specifying alternative HTML if you are embedding the output in an HTML page which you have already started. (For example a routine returning a null string). Returns \&default_start_report (see below) if not set. Example : $index->start_report( \&my_start_report ) Returns : ref to CODE if called without arguments Args : CODE

default_start_report
Title : default_start_report Usage : $self->default_start_report($result) Function: The default method to call when starting a report. Returns : sting Args : First argument is a Bio::Search::Result::ResultI

title
Title : title Usage : $self->title($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report that will appear at the top of the BLAST report HTML output. Useful for (for instance) specifying alternative routines to write your own titles. Returns \&default_title (see below) if not set. Example : $index->title( \&my_title ) Returns : ref to CODE if called without arguments Args : CODE

default_title
Title : default_title Usage : $self->default_title($result) Function: Provides HTML for the given BLAST report that will appear at the top of the BLAST report output. Returns : empty for text implementation Args : First argument is a Bio::Search::Result::ResultI

introduction
Title : introduction Usage : $self->introduction($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report detailing the query and the database information. Useful for (for instance) specifying routines returning alternative introductions. Returns \&default_introduction (see below) if not set. Example : $index->introduction( \&my_introduction ) Returns : ref to CODE if called without arguments Args : CODE

default_introduction
Title : default_introduction Usage : $self->default_introduction($result) Function: Outputs HTML to provide the query and the database information Returns : string containing HTML Args : First argument is a Bio::Search::Result::ResultI Second argument is string holding literature citation

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 (</BODY></HTML>) for HTML Returns : string Args : none

id_parser
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_parser
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_reference
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 : L<Bio::Search::Result::ResultI> to reference

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

no_wublastlinks
Title : no_wublastlinks Usage : $obj->no_wublastlinks($newval) Function: Get/Set boolean value regarding whether or not to display Link = (1) type output in the report output (WU-BLAST only) Returns : boolean Args : on set, new boolean value (a scalar or undef, optional)