# $Id: TilingI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Search::Tiling::TilingI # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module =head1 SYNOPSIS Not used directly. Useful POD here for developers, however. The interface is desgined to make the following code conversion as simple as possible: From: # Bio::Search::SearchUtils-based while ( local $_ = $result->next_hit ) { printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n", $hit->significance, $hit->frac_aligned_query, $hit->num_identical); } To: # TilingI-based while ( local $_ = $result->next_hit ) { my $tiling = Bio::Search::Tiling::MyTiling($_); printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n", $hit->significance, $tiling->frac_aligned_query, $tiling->num_identical); } =head1 DESCRIPTION This module provides strong suggestions for any intended HSP tiling object implementation. An object subclassing TilingI should override the methods defined here according to their descriptions below. See the section STATISTICS METHODS for hints on implementing methods that are valid across different algorithms and report types. =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Tiling::TilingI; use strict; use warnings; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use base qw(Bio::Root::Root); =head2 STATISTICS METHODS The tiling statistics can be thought of as global counterparts to similar statistics defined for the individual HSPs. We therefore prescribe definitions for many of the synonymous methods defined in L. The tiling statistics must be able to keep track of the coordinate systems in which both the query and subject sequences exist; i.e., either nucleotide or amino acid. This information is typically inferred from the name of the algorithm used to perform the original search (contained in C<$hit_object-Ealgorithm>). Here is a table of algorithm information that may be useful (if you trust us). algorithm query on hit coordinates(q/h) --------- ------------ --------------- blastn dna on dna dna/dna blastp aa on aa aa/aa blastx xna on aa dna/aa tblastn aa on xna aa/dna tblastx xna on xna dna/dna fasta dna on dna dna/dna fasta aa on aa aa/aa fastx xna on aa dna/aa fasty xna on aa dna/aa tfasta aa on xna aa/dna tfasty aa on xna aa/dna megablast dna on dna dna/dna xna: translated nucleotide data Statistics methods must also be aware of differences in reporting among the algorithms. Hit attributes are not necessarily normalized over all algorithms. Devs, please feel free to add examples to the list below. =over =item NCBI BLAST vs WU-BLAST (AB-BLAST) lengths The total length of the alignment is reported differently between these two flavors. C<$hit_object-Elength()> will contain the number in the denominator of the stats line; i.e., 120 in Identical = 34/120 Positives = 67/120 NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. "without gaps"). =back Finally, developers should remember that sequence data may or may not be associated with the HSPs contained in the hit object. This will typically depend on whether a full report (e.g, C) or a summary (e.g., C) was parsed. Statistics methods that depend directly on the sequence data will need to check that that data is present. =head2 identities Title : identities Alias : num_identical Usage : $num_identities = $tiling->identities() Function: Return the estimated or exact number of identities in the tiling, accounting for overlapping HSPs Example : Returns : number of identical residue pairs Args : =cut sub identities{ my ($self,@args) = @_; $self->throw_not_implemented; } #HSPI synonym sub num_identical { shift->identities( @_ ) } =head2 conserved Title : conserved Alias : num_conserved Usage : $num_conserved = $tiling->conserved() Function: Return the estimated or exact number of conserved sites in the tiling, accounting for overlapping HSPs Example : Returns : number of conserved residue pairs Args : =cut sub conserved{ my ($self,@args) = @_; $self->throw_not_implemented; } #HSPI synonym sub num_conserved { shift->conserved( @_ ) } =head2 length Title : length Usage : $max_length = $tiling->length($type) Function: Return the total number of residues of the subject or query sequence covered by the tiling Returns : number of "logical" residues covered Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub length{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 frac_identical Title : frac_identical Usage : $tiling->frac_identical($type) Function: Return the fraction of sequence length consisting of identical pairs Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_identical { my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 percent_identity Title : percent_identity Usage : $tiling->percent_identity($type) Function: Return the fraction of sequence length consisting of identical pairs as a percentage Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub percent_identity { my ($self, $type, @args) = @_; return $self->frac_identical($type, @args) * 100; } =head2 frac_conserved Title : frac_conserved Usage : $tiling->frac_conserved($type) Function: Return the fraction of sequence length consisting of conserved pairs Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_conserved{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 percent_conserved Title : percent_conserved Usage : $tiling->percent_conserved($type) Function: Return the fraction of sequence length consisting of conserved pairs as a percentage Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub percent_conserved { my ($self, $type, @args) = @_; return $self->frac_conserved($type, @args) * 100; } =head2 frac_aligned Title : frac_aligned Usage : $tiling->frac_aligned($type) Function: Return the fraction of B sequence length consisting that was aligned by the algorithm Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_aligned{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } # aliases for back compat sub frac_aligned_query { shift->frac_aligned('query', @_) } sub frac_aligned_hit { shift->frac_aligned('hit', @_) } =head2 range Title : range Usage : $tiling->range($type) Function: Returns the extent of the longest tiling as ($min_coord, $max_coord) Returns : array of two scalar integers Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub range { my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head1 TILING ITERATORS =head2 next_tiling Title : next_tiling Usage : @hsps = $self->next_tiling($type); Function: Obtain a tiling of HSPs over the $type ('hit', 'subject', 'query') sequence Example : Returns : an array of HSPI objects Args : scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit' =cut sub next_tiling{ my ($self,$type,@args) = @_; $self->throw_not_implemented; } =head2 rewind_tilings Title : rewind_tilings Usage : $self->rewind_tilings($type) Function: Reset the next_tilings($type) iterator Example : Returns : True on success Args : scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit' =cut sub rewind_tilings{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } #alias sub rewind { shift->rewind_tilings(@_) } =head1 INFORMATIONAL ACCESSORS =head2 algorithm Title : algorithm Usage : $tiling->algorithm Function: Retrieve the algorithm name associated with the invocant's hit object Returns : scalar string Args : =cut sub algorithm{ my ($self, @args) = @_; $self->throw_not_implemented; } 1;