Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects

Example 1: Using the default columns
use Bio::SearchIO; use Bio::SearchIO::Writer::HitTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HitTableWriter->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::HitTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length frac_identical_query expect )] ); my $out = Bio::SearchIO->new( -writer => $writer, -file => ">searchio.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 HitTableWriter 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::HitTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length )], -labels => { 1 => 'QUERY_GI', 3 => 'HIT_IDENTIFIER' } ); Bio::SearchIO::Writer::HitTableWriter outputs summary data for each Hit within a search result. Output is in tab-delimited format, one row per Hit. The reason why this is considered summary data is that if a hit contains multiple HSPs, the HSPs will be tiled and the data represents a summary across all HSPs. See below for which columns are affected. See the docs in Bio::Search::Hit::BlastHit for more details on HSP tiling.

Available Columns
Here are the columns that can be specified in the "-columns" parameter when creating a HitTableWriter object. If a "-columns" parameter is not specified, this list, in this order, will be used as the default. query_name # Sequence identifier of the query. query_length # Full length of the query sequence hit_name # Sequence identifier of the hit hit_length # Full length of the hit sequence round # Round number for hit (PSI-BLAST) expect # Expect value for the alignment score # Score for the alignment (e.g., BLAST score) bits # Bit score for the alignment num_hsps # Number of HSPs (not the "N" value) frac_identical_query* # fraction of identical substitutions in query frac_identical_hit* # fraction of identical substitutions in hit frac_conserved_query* # fraction of conserved substitutions in query frac_conserved_hit* # fraction of conserved substitutions in hit frac_aligned_query* # fraction of the query sequence that is aligned frac_aligned_hit* # fraction of the hit sequence that is aligned length_aln_query* # Length of the aligned portion of the query sequence length_aln_hit* # Length of the aligned portion of the hit sequence gaps_query* # Number of gaps in the aligned query sequence gaps_hit* # Number of gaps in the aligned hit sequence gaps_total* # Number of gaps in the aligned query and hit sequences start_query* # Starting coordinate of the aligned portion of the query sequence end_query* # Ending coordinate of the aligned portion of the query sequence start_hit* # Starting coordinate of the aligned portion of the hit sequence end_hit* # Ending coordinate of the aligned portion of the hit sequence strand_query # Strand of the aligned query sequence strand_hit # Strand of the aligned hit sequence frame # Frame of the alignment (0,1,2) ambiguous_aln # Ambiguous alignment indicator ('qs', 'q', 's') hit_description # Full description of the hit sequence query_description # Full description of the query sequence Items marked with a "*" report data summed across all HSPs after tiling them to avoid counting data from overlapping regions multiple times. For more details about these columns, see the documentation for the corresponding method in Bio::Search::Result::BlastHit. Figure out the best way to incorporate algorithm-specific score columns. The best route is probably to have algorithm-specific subclasses (e.g., BlastHitTableWriter, FastaHitTableWriter).

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/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Steve Chervitz <sac@bioperl.org> See the FEEDBACK section for where to send bug reports and comments. Copyright (c) 2001, 2002 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. This software is provided "as is" without warranty of any kind. Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter

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::BlastResult 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 BlastResult object. Some data is summed across multiple HSPs. : 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